Genes annotated to GO:0031281 using org.Hs.eg.db

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Tim Smith ★ 1.1k

@tim-smith-1532

Last seen 10.2 years ago

Hi, I was trying to get the genes annotated to the GO term "GO:0031281". My code: library(org.Hs.eg.db) genes <- get("GO:0031281", org.Hs.egGO2EG) When I run the code, I get: > genes <- get("GO:0031281", org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : value for "GO:0031281" not found If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? thanks! [[alternative HTML version deleted]]

GO Homo sapiens GO Homo sapiens • 2.3k views

ADD COMMENT • link updated 10.7 years ago by James W. MacDonald 67k • written 10.7 years ago by Tim Smith ★ 1.1k

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James W. MacDonald 67k

@james-w-macdonald-5106

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Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS) IDA IDA TAS TAS IDA TAS IEA TAS TAS TAS "49" "116" "116" "117" "135" "135" "136" "136" "140" "153" IDA IDA TAS IDA IEA IDA IDA TAS IDA IEA "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" "1812" IDA IEA NAS TAS TAS IEA TAS TAS IEA TAS "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" "2778" IDA ISS ISS IBA IBA IMP ISS TAS TAS TAS "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" "5032" ISS NAS IEA IDA IEA TAS TAS "5578" "5894" "7077" "7432" "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL 1 GO:0031281 IDA BP 49 ACR 2 GO:0031281 IDA BP 116 ADCYAP1 3 GO:0031281 TAS BP 116 ADCYAP1 4 GO:0031281 TAS BP 117 ADCYAP1R1 5 GO:0031281 IDA BP 135 ADORA2A 6 GO:0031281 TAS BP 135 ADORA2A 7 GO:0031281 IEA BP 136 ADORA2B 8 GO:0031281 TAS BP 136 ADORA2B 9 GO:0031281 TAS BP 140 ADORA3 10 GO:0031281 TAS BP 153 ADRB1 11 GO:0031281 IDA BP 154 ADRB2 12 GO:0031281 IDA BP 155 ADRB3 13 GO:0031281 TAS BP 554 AVPR2 14 GO:0031281 IDA BP 796 CALCA 15 GO:0031281 IEA BP 796 CALCA 16 GO:0031281 IDA BP 799 CALCR 17 GO:0031281 IDA BP 1394 CRHR1 18 GO:0031281 TAS BP 1394 CRHR1 19 GO:0031281 IDA BP 1812 DRD1 20 GO:0031281 IEA BP 1812 DRD1 21 GO:0031281 IDA BP 1816 DRD5 22 GO:0031281 IEA BP 1816 DRD5 23 GO:0031281 NAS BP 1816 DRD5 24 GO:0031281 TAS BP 1816 DRD5 25 GO:0031281 TAS BP 1909 EDNRA 26 GO:0031281 IEA BP 2692 GHRHR 27 GO:0031281 TAS BP 2696 GIPR 28 GO:0031281 TAS BP 2740 GLP1R 29 GO:0031281 IEA BP 2774 GNAL 30 GO:0031281 TAS BP 2778 GNAS 31 GO:0031281 IDA BP 2852 GPER1 32 GO:0031281 ISS BP 3973 LHCGR 33 GO:0031281 ISS BP 4763 NF1 34 GO:0031281 IBA BP 4842 NOS1 35 GO:0031281 IBA BP 4843 NOS2 36 GO:0031281 IMP BP 4846 NOS3 37 GO:0031281 ISS BP 4846 NOS3 38 GO:0031281 TAS BP 4914 NTRK1 39 GO:0031281 TAS BP 4915 NTRK2 40 GO:0031281 TAS BP 5032 P2RY11 41 GO:0031281 ISS BP 5578 PRKCA 42 GO:0031281 NAS BP 5894 RAF1 43 GO:0031281 IEA BP 7077 TIMP2 44 GO:0031281 IDA BP 7432 VIP 45 GO:0031281 IEA BP 7434 VIPR2 46 GO:0031281 TAS BP 10486 CAP2 47 GO:0031281 TAS BP 10487 CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) : 'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x at ifnotfound) : > value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ADD COMMENT • link 10.7 years ago James W. MacDonald 67k

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Hi James, Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for which I was checking enrichment and I got this term as one of the significant terms. The details are: GOBPID Pvalue OddsRatio ExpCount Count Size Term GO:0031281 0.021301601 10.113271 0.22913929 2 15 positive regulation of cyclase activity I used GOstats for this analysis. If Count = 2, then shouldn't there be two genes that are directly annotated to this term? On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS) IDA IDA TAS TAS IDA TAS IEA TAS TAS TAS "49" "116" "116" "117" "135" "135" "136" "136" "140" "153" IDA IDA TAS IDA IEA IDA IDA TAS IDA IEA "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" "1812" IDA IEA NAS TAS TAS IEA TAS TAS IEA TAS "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" "2778" IDA ISS ISS IBA IBA IMP ISS TAS TAS TAS "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" "5032" ISS NAS IEA IDA IEA TAS TAS "5578" "5894" "7077" "7432" "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL 1 GO:0031281 IDA BP 49 ACR 2 GO:0031281 IDA BP 116 ADCYAP1 3 GO:0031281 TAS BP 116 ADCYAP1 4 GO:0031281 TAS BP 117 ADCYAP1R1 5 GO:0031281 IDA BP 135 ADORA2A 6 GO:0031281 TAS BP 135 ADORA2A 7 GO:0031281 IEA BP 136 ADORA2B 8 GO:0031281 TAS BP 136 ADORA2B 9 GO:0031281 TAS BP 140 ADORA3 10 GO:0031281 TAS BP 153 ADRB1 11 GO:0031281 IDA BP 154 ADRB2 12 GO:0031281 IDA BP 155 ADRB3 13 GO:0031281 TAS BP 554 AVPR2 14 GO:0031281 IDA BP 796 CALCA 15 GO:0031281 IEA BP 796 CALCA 16 GO:0031281 IDA BP 799 CALCR 17 GO:0031281 IDA BP 1394 CRHR1 18 GO:0031281 TAS BP 1394 CRHR1 19 GO:0031281 IDA BP 1812 DRD1 20 GO:0031281 IEA BP 1812 DRD1 21 GO:0031281 IDA BP 1816 DRD5 22 GO:0031281 IEA BP 1816 DRD5 23 GO:0031281 NAS BP 1816 DRD5 24 GO:0031281 TAS BP 1816 DRD5 25 GO:0031281 TAS BP 1909 EDNRA 26 GO:0031281 IEA BP 2692 GHRHR 27 GO:0031281 TAS BP 2696 GIPR 28 GO:0031281 TAS BP 2740 GLP1R 29 GO:0031281 IEA BP 2774 GNAL 30 GO:0031281 TAS BP 2778 GNAS 31 GO:0031281 IDA BP 2852 GPER1 32 GO:0031281 ISS BP 3973 LHCGR 33 GO:0031281 ISS BP 4763 NF1 34 GO:0031281 IBA BP 4842 NOS1 35 GO:0031281 IBA BP 4843 NOS2 36 GO:0031281 IMP BP 4846 NOS3 37 GO:0031281 ISS BP 4846 NOS3 38 GO:0031281 TAS BP 4914 NTRK1 39 GO:0031281 TAS BP 4915 NTRK2 40 GO:0031281 TAS BP 5032 P2RY11 41 GO:0031281 ISS BP 5578 PRKCA 42 GO:0031281 NAS BP 5894 RAF1 43 GO:0031281 IEA BP 7077 TIMP2 44 GO:0031281 IDA BP 7432 VIP 45 GO:0031281 IEA BP 7434 VIPR2 46 GO:0031281 TAS BP 10486 CAP2 47 GO:0031281 TAS BP 10487 CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) : 'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : > value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

ADD REPLY • link 10.7 years ago Tim Smith ★ 1.1k

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Hi James, Hmmm....I seem to get an error if I use probeSetSummary. As I mentioned before I run the hyperGTest using a set of genes (and not a set of probes).Â Here is what I get: hgOverGO <- hyperGTest(paramsGO) > hgOverGO Gene to GO BP Conditional test for over-representationÂ 3843 GO BP ids tested (220 have p < 0.05) Selected gene set size: 318Â Â Â Gene universe size: 6088Â Â Â Annotation package: org.Hs.egÂ > class(hgOverGO) [1] "GOHyperGResult" attr(,"package") [1] "GOstats" > head(summary(hgOverGO)) Â Â Â GOBPID Â Â Â Pvalue OddsRatio Â ExpCount Count Size Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Term 1 GO:0007268 2.658284e-07 Â 2.645556 19.0653745 Â Â 43 Â 365 Â Â Â Â Â Â Â Â Â Â Â Â synaptic transmission 2 GO:0001975 1.299252e-06 21.622722 Â 0.6790407 Â Â 7 Â 13 Â Â Â Â Â Â Â Â Â Â Â response to amphetamine 3 GO:0035637 2.726576e-06 Â 2.320191 22.8784494 Â Â 46 Â 438 Â Â Â Â Â multicellular organismal signaling 4 GO:0072511 1.195032e-05 Â 3.566708 Â 6.2680683 Â Â 19 Â 120 Â Â Â Â Â divalent inorganic cation transport 5 GO:0018958 1.788607e-05 Â 9.280645 Â 1.2536137 Â Â 8 Â 24 phenol- containing compound metabolic process 6 GO:0042886 2.537415e-04 Â 3.066360 Â 5.9546649 Â Â 16 Â 114 Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â amide transport > ps <- probeSetSummary(hgOverGO,pvalue=0.05) Error in (function (classes, fdef, mtable) Â :Â Â unable to find an inherited method for function âcolumnsâ for signature â"function"â > traceback() 7: stop(gettextf("unable to find an inherited method for function %s for signature %s",Â Â Â Â Â sQuote(fdef@generic), sQuote(cnames)), domain = NA) 6: (function (classes, fdef, mtable)Â Â Â { Â Â Â Â methods <- .findInheritedMethods(classes, fdef, mtable) Â Â Â Â if (length(methods) == 1L)Â Â Â Â Â Â Â return(methods[[1L]]) Â Â Â Â else if (length(methods) == 0L) { Â Â Â Â Â Â cnames <- paste0("\"", sapply(classes, as.character),Â Â Â Â Â Â Â Â Â "\"", collapse = ", ") Â Â Â Â Â Â stop(gettextf("unable to find an inherited method for function %s for signature %s",Â Â Â Â Â Â Â Â Â sQuote(fdef@generic), sQuote(cnames)), domain = NA) Â Â Â Â } Â Â Â Â else stop("Internal error in finding inherited methods; didn't return a unique method",Â Â Â Â Â Â Â domain = NA) Â Â })(list("function"), function (x)Â Â Â standardGeneric("columns"), <environment>) 5: columns(db) 4: match(x, table, nomatch = 0L) 3: map %in% columns(db) 2: getAnnMap(ids, annotation(result)) 1: probeSetSummary(hgOverGO, pvalue = 0.05) Am I calling the probeSetSummary function incorrectly? thanks!! On Wednesday, March 19, 2014 5:54 PM, Tim Smith <tim_smith_666@yahoo.com> wrote: Hi James, Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for which I was checking enrichment and I got this term as one of the significant terms. The details are: Â Â Â Â Â Â Â Â GOBPIDÂ Â Â Pvalue OddsRatioÂ Â ExpCount Count SizeÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Term GO:0031281 0.021301601 10.113271Â 0.22913929 Â Â 2 Â 15 Â Â Â Â Â Â Â Â Â Â Â Â Â positive regulation of cyclase activity I used GOstats for this analysis. If Count = 2, then shouldn't there be two genes that are directly annotated to this term? On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS) Â Â Â IDAÂ Â Â IDAÂ Â Â TASÂ Â Â TASÂ Â Â IDAÂ Â Â TASÂ Â Â IEAÂ Â Â TAS TASÂ Â TAS Â Â "49"Â Â "116"Â Â "116"Â Â "117"Â Â "135"Â Â "135"Â Â "136"Â Â "136" "140"Â "153" Â Â Â IDAÂ Â Â IDAÂ Â Â TASÂ Â Â IDAÂ Â Â IEAÂ Â Â IDAÂ Â Â IDAÂ Â Â TAS IDAÂ Â IEA Â Â "154"Â Â "155"Â Â "554"Â Â "796"Â Â "796"Â Â "799"Â "1394"Â "1394" "1812"Â "1812" Â Â Â IDAÂ Â Â IEAÂ Â Â NASÂ Â Â TASÂ Â Â TASÂ Â Â IEAÂ Â Â TASÂ Â Â TAS IEAÂ Â TAS Â "1816"Â "1816"Â "1816"Â "1816"Â "1909"Â "2692"Â "2696"Â "2740" "2774"Â "2778" Â Â Â IDAÂ Â Â ISSÂ Â Â ISSÂ Â Â IBAÂ Â Â IBAÂ Â Â IMPÂ Â Â ISSÂ Â Â TAS TASÂ Â TAS Â "2852"Â "3973"Â "4763"Â "4842"Â "4843"Â "4846"Â "4846"Â "4914" "4915"Â "5032" Â Â Â ISSÂ Â Â NASÂ Â Â IEAÂ Â Â IDAÂ Â Â IEAÂ Â Â TASÂ Â Â TAS Â "5578"Â "5894"Â "7077"Â "7432"Â "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") Â Â Â Â Â GOALL EVIDENCEALL ONTOLOGYALL ENTREZIDÂ Â SYMBOL 1Â GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â Â 49Â Â Â Â ACR 2Â GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 116Â Â ADCYAP1 3Â GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 116Â Â ADCYAP1 4Â GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 117 ADCYAP1R1 5Â GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 135Â Â ADORA2A 6Â GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 135Â Â ADORA2A 7Â GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 136Â Â ADORA2B 8Â GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 136Â Â ADORA2B 9Â GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 140Â Â ADORA3 10 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 153Â Â Â ADRB1 11 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 154Â Â Â ADRB2 12 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 155Â Â Â ADRB3 13 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 554Â Â Â AVPR2 14 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 796Â Â Â CALCA 15 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 796Â Â Â CALCA 16 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 799Â Â Â CALCR 17 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 1394Â Â Â CRHR1 18 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 1394Â Â Â CRHR1 19 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 1812Â Â Â DRD1 20 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 1812Â Â Â DRD1 21 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 1816Â Â Â DRD5 22 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 1816Â Â Â DRD5 23 GO:0031281Â Â Â Â Â NASÂ Â Â Â Â BPÂ Â Â 1816Â Â Â DRD5 24 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 1816Â Â Â DRD5 25 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 1909Â Â Â EDNRA 26 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 2692Â Â Â GHRHR 27 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 2696Â Â Â GIPR 28 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 2740Â Â Â GLP1R 29 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 2774Â Â Â GNAL 30 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 2778Â Â Â GNAS 31 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 2852Â Â Â GPER1 32 GO:0031281Â Â Â Â Â ISSÂ Â Â Â Â BPÂ Â Â 3973Â Â Â LHCGR 33 GO:0031281Â Â Â Â Â ISSÂ Â Â Â Â BPÂ Â Â 4763Â Â Â Â NF1 34 GO:0031281Â Â Â Â Â IBAÂ Â Â Â Â BPÂ Â Â 4842Â Â Â NOS1 35 GO:0031281Â Â Â Â Â IBAÂ Â Â Â Â BPÂ Â Â 4843Â Â Â NOS2 36 GO:0031281Â Â Â Â Â IMPÂ Â Â Â Â BPÂ Â Â 4846Â Â Â NOS3 37 GO:0031281Â Â Â Â Â ISSÂ Â Â Â Â BPÂ Â Â 4846Â Â Â NOS3 38 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 4914Â Â Â NTRK1 39 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 4915Â Â Â NTRK2 40 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 5032Â Â P2RY11 41 GO:0031281Â Â Â Â Â ISSÂ Â Â Â Â BPÂ Â Â 5578Â Â Â PRKCA 42 GO:0031281Â Â Â Â Â NASÂ Â Â Â Â BPÂ Â Â 5894Â Â Â RAF1 43 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 7077Â Â Â TIMP2 44 GO:0031281Â Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 7432Â Â Â Â VIP 45 GO:0031281Â Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 7434Â Â Â VIPR2 46 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10486Â Â Â CAP2 47 GO:0031281Â Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10487Â Â Â CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) : Â Â 'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : >Â Â value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! > Â Â Â [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 Â Â Â [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD REPLY • link 10.7 years ago Tim Smith ★ 1.1k

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Hi Tim, Note that you _always_ use a set of genes for hyperGTest. Even if you started with an array, you can only count a significantly differentially expressed gene once. The difference here is that you used the org.Hs.eg.db package as the annotation rather than some array annotation package, so probeSetSummary() won't work, as it is trying to match things back to probe IDs. So you can do something like this: gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") gos <- summary(hgOverGO)[,1] golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) Best, Jim On 3/19/2014 7:03 PM, Tim Smith wrote: > Hi James, > > Hmmm....I seem to get an error if I use probeSetSummary. As I > mentioned before I run the hyperGTest using a set of genes (and not a > set of probes). > > Here is what I get: > > hgOverGO <- hyperGTest(paramsGO) > > > hgOverGO > Gene to GO BP Conditional test for over-representation > 3843 GO BP ids tested (220 have p < 0.05) > Selected gene set size: 318 > Gene universe size: 6088 > Annotation package: org.Hs.eg > > > class(hgOverGO) > [1] "GOHyperGResult" > attr(,"package") > [1] "GOstats" > > > head(summary(hgOverGO)) > GOBPID Pvalue OddsRatio ExpCount Count Size Term > 1 GO:0007268 2.658284e-07 2.645556 19.0653745 43 365 > synaptic transmission > 2 GO:0001975 1.299252e-06 21.622722 0.6790407 7 13 response > to amphetamine > 3 GO:0035637 2.726576e-06 2.320191 22.8784494 46 438 > multicellular organismal signaling > 4 GO:0072511 1.195032e-05 3.566708 6.2680683 19 120 > divalent inorganic cation transport > 5 GO:0018958 1.788607e-05 9.280645 1.2536137 8 24 > phenol-containing compound metabolic process > 6 GO:0042886 2.537415e-04 3.066360 5.9546649 16 114 > amide transport > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?columns? for > signature ?"function"? > > > traceback() > 7: stop(gettextf("unable to find an inherited method for function %s > for signature %s", > sQuote(fdef at generic), sQuote(cnames)), domain = NA) > 6: (function (classes, fdef, mtable) > { > methods <- .findInheritedMethods(classes, fdef, mtable) > if (length(methods) == 1L) > return(methods[[1L]]) > else if (length(methods) == 0L) { > cnames <- paste0("\"", sapply(classes, as.character), > "\"", collapse = ", ") > stop(gettextf("unable to find an inherited method for function %s for > signature %s", > sQuote(fdef at generic), sQuote(cnames)), domain = NA) > } > else stop("Internal error in finding inherited methods; didn't > return a unique method", > domain = NA) > })(list("function"), function (x) > standardGeneric("columns"), <environment>) > 5: columns(db) > 4: match(x, table, nomatch = 0L) > 3: map %in% columns(db) > 2: getAnnMap(ids, annotation(result)) > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > Am I calling the probeSetSummary function incorrectly? > > > thanks!! > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > <tim_smith_666 at="" yahoo.com=""> wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > > GOBPID Pvalue OddsRatio ExpCount Count Size > Term > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">> wrote: > > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > IDA IDA TAS TAS IDA TAS IEA TAS TAS > TAS > "49" "116" "116" "117" "135" "135" "136" "136" "140" > "153" > IDA IDA TAS IDA IEA IDA IDA TAS IDA > IEA > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > "1812" > IDA IEA NAS TAS TAS IEA TAS TAS IEA > TAS > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > "2778" > IDA ISS ISS IBA IBA IMP ISS TAS TAS > TAS > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > "5032" > ISS NAS IEA IDA IEA TAS TAS > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1 GO:0031281 IDA BP 49 ACR > 2 GO:0031281 IDA BP 116 ADCYAP1 > 3 GO:0031281 TAS BP 116 ADCYAP1 > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > 5 GO:0031281 IDA BP 135 ADORA2A > 6 GO:0031281 TAS BP 135 ADORA2A > 7 GO:0031281 IEA BP 136 ADORA2B > 8 GO:0031281 TAS BP 136 ADORA2B > 9 GO:0031281 TAS BP 140 ADORA3 > 10 GO:0031281 TAS BP 153 ADRB1 > 11 GO:0031281 IDA BP 154 ADRB2 > 12 GO:0031281 IDA BP 155 ADRB3 > 13 GO:0031281 TAS BP 554 AVPR2 > 14 GO:0031281 IDA BP 796 CALCA > 15 GO:0031281 IEA BP 796 CALCA > 16 GO:0031281 IDA BP 799 CALCR > 17 GO:0031281 IDA BP 1394 CRHR1 > 18 GO:0031281 TAS BP 1394 CRHR1 > 19 GO:0031281 IDA BP 1812 DRD1 > 20 GO:0031281 IEA BP 1812 DRD1 > 21 GO:0031281 IDA BP 1816 DRD5 > 22 GO:0031281 IEA BP 1816 DRD5 > 23 GO:0031281 NAS BP 1816 DRD5 > 24 GO:0031281 TAS BP 1816 DRD5 > 25 GO:0031281 TAS BP 1909 EDNRA > 26 GO:0031281 IEA BP 2692 GHRHR > 27 GO:0031281 TAS BP 2696 GIPR > 28 GO:0031281 TAS BP 2740 GLP1R > 29 GO:0031281 IEA BP 2774 GNAL > 30 GO:0031281 TAS BP 2778 GNAS > 31 GO:0031281 IDA BP 2852 GPER1 > 32 GO:0031281 ISS BP 3973 LHCGR > 33 GO:0031281 ISS BP 4763 NF1 > 34 GO:0031281 IBA BP 4842 NOS1 > 35 GO:0031281 IBA BP 4843 NOS2 > 36 GO:0031281 IMP BP 4846 NOS3 > 37 GO:0031281 ISS BP 4846 NOS3 > 38 GO:0031281 TAS BP 4914 NTRK1 > 39 GO:0031281 TAS BP 4915 NTRK2 > 40 GO:0031281 TAS BP 5032 P2RY11 > 41 GO:0031281 ISS BP 5578 PRKCA > 42 GO:0031281 NAS BP 5894 RAF1 > 43 GO:0031281 IEA BP 7077 TIMP2 > 44 GO:0031281 IDA BP 7432 VIP > 45 GO:0031281 IEA BP 7434 VIPR2 > 46 GO:0031281 TAS BP 10486 CAP2 > 47 GO:0031281 TAS BP 10487 CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : > 'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound="">) : > > value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ADD REPLY • link 10.7 years ago James W. MacDonald 67k

1

Entering edit mode

Hi James, Thanks for that. However, the number of genes associated with the GO term with your code example, doesn't match the number of genes associated with that GO term with summary(hgOverGO): For example, my hgOverGO gives 43 genes annotated to the node: GOBPID Pvalue OddsRatio ExpCount Count Size Term GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 365 synaptic transmission While if I use your example code, it results in 53 genes. There are many such mismatches. Wouldn't it be great if GOstats gives the option of accessing the actual genes that it found annotated to a GO term? thanks !! On Thursday, March 20, 2014 10:38 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, Note that you _always_ use a set of genes for hyperGTest. Even if you started with an array, you can only count a significantly differentially expressed gene once. The difference here is that you used the org.Hs.eg.db package as the annotation rather than some array annotation package, so probeSetSummary() won't work, as it is trying to match things back to probe IDs. So you can do something like this: gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") gos <- summary(hgOverGO)[,1] golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) Best, Jim On 3/19/2014 7:03 PM, Tim Smith wrote: > Hi James, > > Hmmm....I seem to get an error if I use probeSetSummary. As I > mentioned before I run the hyperGTest using a set of genes (and not a > set of probes). > > Here is what I get: > > hgOverGO <- hyperGTest(paramsGO) > > > hgOverGO > Gene to GO BP Conditional test for over-representation > 3843 GO BP ids tested (220 have p < 0.05) > Selected gene set size: 318 >Â Â Gene universe size: 6088 >Â Â Annotation package: org.Hs.eg > > > class(hgOverGO) > [1] "GOHyperGResult" > attr(,"package") > [1] "GOstats" > > > head(summary(hgOverGO)) >Â Â Â GOBPID Pvalue OddsRatioÂ ExpCount Count SizeÂ Â Â Â Â Â Â Â Term > 1 GO:0007268 2.658284e-07Â 2.645556 19.0653745Â Â 43Â 365Â Â >Â synaptic transmission > 2 GO:0001975 1.299252e-06 21.622722Â 0.6790407Â Â 7Â 13Â Â response > to amphetamine > 3 GO:0035637 2.726576e-06Â 2.320191 22.8784494Â Â 46Â 438 > multicellular organismal signaling > 4 GO:0072511 1.195032e-05Â 3.566708Â 6.2680683Â Â 19Â 120Â Â Â Â >Â divalent inorganic cation transport > 5 GO:0018958 1.788607e-05Â 9.280645Â 1.2536137Â Â 8Â 24 > phenol-containing compound metabolic process > 6 GO:0042886 2.537415e-04Â 3.066360Â 5.9546649Â Â 16Â 114Â Â Â Â Â >Â amide transport > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > Error in (function (classes, fdef, mtable)Â : >Â unable to find an inherited method for function âcolumnsâ for > signature â"function"â > > > traceback() > 7: stop(gettextf("unable to find an inherited method for function %s > for signature %s", >Â sQuote(fdef@generic), sQuote(cnames)), domain = NA) > 6: (function (classes, fdef, mtable) >Â Â { >Â Â Â Â methods <- .findInheritedMethods(classes, fdef, mtable) >Â Â Â Â if (length(methods) == 1L) >Â return(methods[[1L]]) >Â Â Â Â else if (length(methods) == 0L) { >Â Â Â Â Â Â cnames <- paste0("\"", sapply(classes, as.character), >Â Â Â Â Â Â Â Â "\"", collapse = ", ") >Â stop(gettextf("unable to find an inherited method for function %s for > signature %s", >Â sQuote(fdef@generic), sQuote(cnames)), domain = NA) >Â Â Â Â } >Â Â Â Â else stop("Internal error in finding inherited methods; didn't > return a unique method", >Â Â Â Â Â Â domain = NA) >Â })(list("function"), function (x) >Â standardGeneric("columns"), <environment>) > 5: columns(db) > 4: match(x, table, nomatch = 0L) > 3: map %in% columns(db) > 2: getAnnMap(ids, annotation(result)) > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > Am I calling the probeSetSummary function incorrectly? > > > thanks!! > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > <tim_smith_666@yahoo.com> wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > >Â Â Â Â Â Â Â Â GOBPIDÂ Â Â Pvalue OddsRatioÂ Â ExpCount Count SizeÂ Â >Â Â Â Â Â Â Term > GO:0031281 0.021301601 10.113271Â 0.22913929Â Â 2Â 15Â Â Â Â Â Â Â >Â Â Â Â Â Â positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon@uw.edu <mailto:jmacdon@uw.edu="">> wrote: > > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) >Â Â Â IDAÂ Â IDAÂ Â TASÂ Â TASÂ Â IDAÂ Â TAS IEAÂ Â TAS TAS > TAS >Â Â "49"Â "116"Â "116"Â "117"Â "135"Â "135" "136"Â "136" "140" > "153" >Â Â Â IDAÂ Â IDAÂ Â TASÂ Â IDAÂ Â IEAÂ Â IDA IDAÂ Â TAS IDA > IEA >Â Â "154"Â "155"Â "554"Â "796"Â "796"Â "799" "1394"Â "1394" "1812" > "1812" >Â Â Â IDAÂ Â IEAÂ Â NASÂ Â TASÂ Â TASÂ Â IEA TASÂ Â TAS IEA > TAS >Â "1816"Â "1816"Â "1816"Â "1816"Â "1909"Â "2692" "2696"Â "2740" "2774" > "2778" >Â Â Â IDAÂ Â ISSÂ Â ISSÂ Â IBAÂ Â IBAÂ Â IMP ISSÂ Â TAS TAS > TAS >Â "2852"Â "3973"Â "4763"Â "4842"Â "4843"Â "4846" "4846"Â "4914" "4915" > "5032" >Â Â Â ISSÂ Â NASÂ Â IEAÂ Â IDAÂ Â IEAÂ Â TASÂ Â TAS >Â "5578"Â "5894"Â "7077"Â "7432"Â "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") >Â Â Â Â Â GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 49Â Â Â ACR > 2Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 116Â ADCYAP1 > 3Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 116Â ADCYAP1 > 4Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 117 ADCYAP1R1 > 5Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 135Â ADORA2A > 6Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 135Â ADORA2A > 7Â GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 136Â ADORA2B > 8Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 136Â ADORA2B > 9Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 140Â Â ADORA3 > 10 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 153Â Â ADRB1 > 11 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 154Â Â ADRB2 > 12 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 155Â Â ADRB3 > 13 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 554Â Â AVPR2 > 14 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 796Â Â CALCA > 15 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 796Â Â CALCA > 16 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 799Â Â CALCR > 17 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1394Â Â CRHR1 > 18 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1394Â Â CRHR1 > 19 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1812Â Â Â DRD1 > 20 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 1812Â Â Â DRD1 > 21 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1816Â Â Â DRD5 > 22 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 1816Â Â Â DRD5 > 23 GO:0031281Â Â Â Â NASÂ Â Â Â Â BPÂ Â 1816Â Â Â DRD5 > 24 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1816Â Â Â DRD5 > 25 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1909Â Â EDNRA > 26 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 2692Â Â GHRHR > 27 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2696Â Â Â GIPR > 28 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2740Â Â GLP1R > 29 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 2774Â Â Â GNAL > 30 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2778Â Â Â GNAS > 31 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 2852Â Â GPER1 > 32 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 3973Â Â LHCGR > 33 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 4763Â Â Â NF1 > 34 GO:0031281Â Â Â Â IBAÂ Â Â Â Â BPÂ Â 4842Â Â Â NOS1 > 35 GO:0031281Â Â Â Â IBAÂ Â Â Â Â BPÂ Â 4843Â Â Â NOS2 > 36 GO:0031281Â Â Â Â IMPÂ Â Â Â Â BPÂ Â 4846Â Â Â NOS3 > 37 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 4846Â Â Â NOS3 > 38 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 4914Â Â NTRK1 > 39 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 4915Â Â NTRK2 > 40 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 5032Â Â P2RY11 > 41 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 5578Â Â PRKCA > 42 GO:0031281Â Â Â Â NASÂ Â Â Â Â BPÂ Â 5894Â Â Â RAF1 > 43 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 7077Â Â TIMP2 > 44 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 7432Â Â Â VIP > 45 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 7434Â Â VIPR2 > 46 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10486Â Â Â CAP2 > 47 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10487Â Â Â CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : >Â Â 'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x@ifnotfound > <mailto:x@ifnotfound>) : > >Â Â value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > >Â Â [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > >Â Â [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

ADD REPLY • link 10.7 years ago Tim Smith ★ 1.1k

0

Entering edit mode

Hi Tim, Different approach. gos <- summary(hgOverGO)[,1] gIU <- geneIdUniverse(hgOverGO)[gos] gns <- geneIds(hgOverGO) golst <- lapply(gIU, function(x) x[x %in% gns]) And as a test > univ <- keys(org.Hs.eg.db) > set.seed(0xabeef) > gns <- sample(300, univ) > p <- new(:GOHyperGParams, geneIds = gns, universeGeneIds = univ, ontology = "BP", annotation = "org.Hs.eg.db") > hyp <- hyperGTest(p) > gos <- summary(hyp)[,1] > gIU <- geneIdUniverse(hyp)[gos] > golst <- lapply(gIU, function(x) x[x %in% gns]) > all.equal(summary(hyp)[,"Count"], sapply(golst, length), check.attributes = FALSE) [1] TRUE Best, Jim On 3/21/2014 8:12 PM, Tim Smith wrote: > Hi James, > > Thanks for that. However, the number of genes associated with the GO > term with your code example, doesn't match the number of genes > associated with that GO term with summary(hgOverGO): > > For example, my hgOverGO gives 43 genes annotated to the node: > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 > 365 synaptic transmission > > While if I use your example code, it results in 53 genes. There are > many such mismatches. Wouldn't it be great if GOstats gives the option > of accessing the actual genes that it found annotated to a GO term? > > thanks !! > > > > > > > On Thursday, March 20, 2014 10:38 AM, James W. MacDonald > <jmacdon at="" uw.edu=""> wrote: > Hi Tim, > > Note that you _always_ use a set of genes for hyperGTest. Even if you > started with an array, you can only count a significantly differentially > expressed gene once. > > The difference here is that you used the org.Hs.eg.db package as the > annotation rather than some array annotation package, so > probeSetSummary() won't work, as it is trying to match things back to > probe IDs. > > So you can do something like this: > > gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") > gos <- summary(hgOverGO)[,1] > golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) > > Best, > > Jim > > > > On 3/19/2014 7:03 PM, Tim Smith wrote: > > Hi James, > > > > Hmmm....I seem to get an error if I use probeSetSummary. As I > > mentioned before I run the hyperGTest using a set of genes (and not a > > set of probes). > > > > Here is what I get: > > > > hgOverGO <- hyperGTest(paramsGO) > > > > > hgOverGO > > Gene to GO BP Conditional test for over-representation > > 3843 GO BP ids tested (220 have p < 0.05) > > Selected gene set size: 318 > > Gene universe size: 6088 > > Annotation package: org.Hs.eg > > > > > class(hgOverGO) > > [1] "GOHyperGResult" > > attr(,"package") > > [1] "GOstats" > > > > > head(summary(hgOverGO)) > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > > 1 GO:0007268 2.658284e-07 2.645556 19.0653745 43 365 > > synaptic transmission > > 2 GO:0001975 1.299252e-06 21.622722 0.6790407 7 13 response > > to amphetamine > > 3 GO:0035637 2.726576e-06 2.320191 22.8784494 46 438 > > multicellular organismal signaling > > 4 GO:0072511 1.195032e-05 3.566708 6.2680683 19 120 > > divalent inorganic cation transport > > 5 GO:0018958 1.788607e-05 9.280645 1.2536137 8 24 > > phenol-containing compound metabolic process > > 6 GO:0042886 2.537415e-04 3.066360 5.9546649 16 114 > > amide transport > > > > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > > Error in (function (classes, fdef, mtable) : > > unable to find an inherited method for function ?columns? for > > signature ?"function"? > > > > > traceback() > > 7: stop(gettextf("unable to find an inherited method for function %s > > for signature %s", > > sQuote(fdef at generic <mailto:fdef at="" generic="">), sQuote(cnames)), domain > = NA) > > 6: (function (classes, fdef, mtable) > > { > > methods <- .findInheritedMethods(classes, fdef, mtable) > > if (length(methods) == 1L) > > return(methods[[1L]]) > > else if (length(methods) == 0L) { > > cnames <- paste0("\"", sapply(classes, as.character), > > "\"", collapse = ", ") > > stop(gettextf("unable to find an inherited method for function %s for > > signature %s", > > sQuote(fdef at generic <mailto:fdef at="" generic="">), sQuote(cnames)), domain > = NA) > > } > > else stop("Internal error in finding inherited methods; didn't > > return a unique method", > > domain = NA) > > })(list("function"), function (x) > > standardGeneric("columns"), <environment>) > > 5: columns(db) > > 4: match(x, table, nomatch = 0L) > > 3: map %in% columns(db) > > 2: getAnnMap(ids, annotation(result)) > > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > > > > Am I calling the probeSetSummary function incorrectly? > > > > > > thanks!! > > > > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > > <tim_smith_666 at="" yahoo.com="" <mailto:tim_smith_666="" at="" yahoo.com="">> wrote: > > Hi James, > > > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > > which I was checking enrichment and I got this term as one of the > > significant terms. The details are: > > > > GOBPID Pvalue OddsRatio ExpCount Count Size > > Term > > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > > positive regulation of cyclase activity > > > > I used GOstats for this analysis. If Count = 2, then shouldn't there > > be two genes that are directly annotated to this term? > > > > > > > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > > > Hi Tim, > > > > There may not be any IDs mapped to that term directly. You can use > > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > > IDA IDA TAS TAS IDA TAS IEA TAS TAS > > TAS > > "49" "116" "116" "117" "135" "135" "136" "136" "140" > > "153" > > IDA IDA TAS IDA IEA IDA IDA TAS IDA > > IEA > > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > > "1812" > > IDA IEA NAS TAS TAS IEA TAS TAS IEA > > TAS > > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > > "2778" > > IDA ISS ISS IBA IBA IMP ISS TAS TAS > > TAS > > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > > "5032" > > ISS NAS IEA IDA IEA TAS TAS > > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > > > Or the more powerful select() method: > > > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > > 1 GO:0031281 IDA BP 49 ACR > > 2 GO:0031281 IDA BP 116 ADCYAP1 > > 3 GO:0031281 TAS BP 116 ADCYAP1 > > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > > 5 GO:0031281 IDA BP 135 ADORA2A > > 6 GO:0031281 TAS BP 135 ADORA2A > > 7 GO:0031281 IEA BP 136 ADORA2B > > 8 GO:0031281 TAS BP 136 ADORA2B > > 9 GO:0031281 TAS BP 140 ADORA3 > > 10 GO:0031281 TAS BP 153 ADRB1 > > 11 GO:0031281 IDA BP 154 ADRB2 > > 12 GO:0031281 IDA BP 155 ADRB3 > > 13 GO:0031281 TAS BP 554 AVPR2 > > 14 GO:0031281 IDA BP 796 CALCA > > 15 GO:0031281 IEA BP 796 CALCA > > 16 GO:0031281 IDA BP 799 CALCR > > 17 GO:0031281 IDA BP 1394 CRHR1 > > 18 GO:0031281 TAS BP 1394 CRHR1 > > 19 GO:0031281 IDA BP 1812 DRD1 > > 20 GO:0031281 IEA BP 1812 DRD1 > > 21 GO:0031281 IDA BP 1816 DRD5 > > 22 GO:0031281 IEA BP 1816 DRD5 > > 23 GO:0031281 NAS BP 1816 DRD5 > > 24 GO:0031281 TAS BP 1816 DRD5 > > 25 GO:0031281 TAS BP 1909 EDNRA > > 26 GO:0031281 IEA BP 2692 GHRHR > > 27 GO:0031281 TAS BP 2696 GIPR > > 28 GO:0031281 TAS BP 2740 GLP1R > > 29 GO:0031281 IEA BP 2774 GNAL > > 30 GO:0031281 TAS BP 2778 GNAS > > 31 GO:0031281 IDA BP 2852 GPER1 > > 32 GO:0031281 ISS BP 3973 LHCGR > > 33 GO:0031281 ISS BP 4763 NF1 > > 34 GO:0031281 IBA BP 4842 NOS1 > > 35 GO:0031281 IBA BP 4843 NOS2 > > 36 GO:0031281 IMP BP 4846 NOS3 > > 37 GO:0031281 ISS BP 4846 NOS3 > > 38 GO:0031281 TAS BP 4914 NTRK1 > > 39 GO:0031281 TAS BP 4915 NTRK2 > > 40 GO:0031281 TAS BP 5032 P2RY11 > > 41 GO:0031281 ISS BP 5578 PRKCA > > 42 GO:0031281 NAS BP 5894 RAF1 > > 43 GO:0031281 IEA BP 7077 TIMP2 > > 44 GO:0031281 IDA BP 7432 VIP > > 45 GO:0031281 IEA BP 7434 VIPR2 > > 46 GO:0031281 TAS BP 10486 CAP2 > > 47 GO:0031281 TAS BP 10487 CAP1 > > Warning message: > > In .generateExtraRows(tab, keys, jointype) : > > 'select' resulted in 1:many mapping between keys and return rows > > > > Best, > > > > Jim > > > > > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > > Hi, > > > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > > My code: > > > > > > library(org.Hs.eg.db) > > > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > > > When I run the code, I get: > > > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound=""> > > <mailto:x at="" ifnotfound="" <mailto:x="" at="" ifnotfound="">>) : > > > value for "GO:0031281" not found > > > > > > If I check in AMIGO for this GO term, it seems to have many gene > > products for Homo sapiens. Am I doing something wrong? Is there an > > alternate package that I can try, just to double check the results? > > > > > > thanks! > > > [[alternative HTML version deleted]] > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ADD REPLY • link 10.7 years ago James W. MacDonald 67k

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Thanks Jim - Â I think you've cracked it!! On Monday, March 24, 2014 12:01 PM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, Different approach. gos <- summary(hgOverGO)[,1] gIU <- geneIdUniverse(hgOverGO)[gos] gns <- geneIds(hgOverGO) golst <- lapply(gIU, function(x) x[x %in% gns]) And as a test > univ <- keys(org.Hs.eg.db) > set.seed(0xabeef) > gns <- sample(300, univ) > p <- new(:GOHyperGParams, geneIds = gns, universeGeneIds = univ, ontology = "BP", annotation = "org.Hs.eg.db") > hyp <- hyperGTest(p) > gos <- summary(hyp)[,1] > gIU <- geneIdUniverse(hyp)[gos] > golst <- lapply(gIU, function(x) x[x %in% gns]) > all.equal(summary(hyp)[,"Count"], sapply(golst, length), check.attributes = FALSE) [1] TRUE Best, Jim On 3/21/2014 8:12 PM, Tim Smith wrote: > Hi James, > > Thanks for that. However, the number of genes associated with the GO > term with your code example, doesn't match the number of genes > associated with that GO term with summary(hgOverGO): > > For example, my hgOverGO gives 43 genes annotated to the node: > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 > 365 synaptic transmission > > While if I use your example code, it results in 53 genes. There are > many such mismatches. Wouldn't it be great if GOstats gives the option > of accessing the actual genes that it found annotated to a GO term? > > thanks !! > > > > > > > On Thursday, March 20, 2014 10:38 AM, James W. MacDonald > <jmacdon@uw.edu> wrote: > Hi Tim, > > Note that you _always_ use a set of genes for hyperGTest. Even if you > started with an array, you can only count a significantly differentially > expressed gene once. > > The difference here is that you used the org.Hs.eg.db package as the > annotation rather than some array annotation package, so > probeSetSummary() won't work, as it is trying to match things back to > probe IDs. > > So you can do something like this: > > gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") > gos <- summary(hgOverGO)[,1] > golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) > > Best, > > Jim > > > > On 3/19/2014 7:03 PM, Tim Smith wrote: > > Hi James, > > > > Hmmm....I seem to get an error if I use probeSetSummary. As I > > mentioned before I run the hyperGTest using a set of genes (and not a > > set of probes). > > > > Here is what I get: > > > > hgOverGO <- hyperGTest(paramsGO) > > > > > hgOverGO > > Gene to GO BP Conditional test for over-representation > > 3843 GO BP ids tested (220 have p < 0.05) > > Selected gene set size: 318 > >Â Â Gene universe size: 6088 > >Â Â Annotation package: org.Hs.eg > > > > > class(hgOverGO) > > [1] "GOHyperGResult" > > attr(,"package") > > [1] "GOstats" > > > > > head(summary(hgOverGO)) > >Â Â Â GOBPID Pvalue OddsRatioÂ ExpCount Count SizeÂ Â Â Â Â Â Â Term > > 1 GO:0007268 2.658284e-07Â 2.645556 19.0653745 43Â 365 > >Â synaptic transmission > > 2 GO:0001975 1.299252e-06 21.622722Â 0.6790407 7Â 13Â Â response > > to amphetamine > > 3 GO:0035637 2.726576e-06Â 2.320191 22.8784494 46Â 438 > > multicellular organismal signaling > > 4 GO:0072511 1.195032e-05Â 3.566708Â 6.2680683 19Â 120 > >Â divalent inorganic cation transport > > 5 GO:0018958 1.788607e-05Â 9.280645Â 1.2536137 8Â 24 > > phenol-containing compound metabolic process > > 6 GO:0042886 2.537415e-04Â 3.066360Â 5.9546649 16Â 114 > >Â amide transport > > > > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > > Error in (function (classes, fdef, mtable)Â : > >Â unable to find an inherited method for function âcolumnsâ for > > signature â"function"â > > > > > traceback() > > 7: stop(gettextf("unable to find an inherited method for function %s > > for signature %s", > >Â sQuote(fdef@generic <mailto:fdef@generic>), sQuote(cnames)), domain > = NA) > > 6: (function (classes, fdef, mtable) > >Â Â { > >Â Â Â Â methods <- .findInheritedMethods(classes, fdef, mtable) > >Â Â Â Â if (length(methods) == 1L) > >Â return(methods[[1L]]) > >Â Â Â Â else if (length(methods) == 0L) { > >Â Â Â Â Â Â cnames <- paste0("\"", sapply(classes, as.character), > >Â Â Â Â Â Â Â Â "\"", collapse = ", ") > >Â stop(gettextf("unable to find an inherited method for function %s for > > signature %s", > >Â sQuote(fdef@generic <mailto:fdef@generic>), sQuote(cnames)), domain > = NA) > >Â Â Â Â } > >Â Â Â Â else stop("Internal error in finding inherited methods; didn't > > return a unique method", > >Â Â Â Â Â Â domain = NA) > >Â })(list("function"), function (x) > >Â standardGeneric("columns"), <environment>) > > 5: columns(db) > > 4: match(x, table, nomatch = 0L) > > 3: map %in% columns(db) > > 2: getAnnMap(ids, annotation(result)) > > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > > > > Am I calling the probeSetSummary function incorrectly? > > > > > > thanks!! > > > > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > > <tim_smith_666@yahoo.com <mailto:tim_smith_666@yahoo.com="">> wrote: > > Hi James, > > > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > > which I was checking enrichment and I got this term as one of the > > significant terms. The details are: > > > >Â Â Â Â Â Â Â Â GOBPIDÂ Â Â Pvalue OddsRatio ExpCount Count Size > >Â Â Â Â Â Â Term > > GO:0031281 0.021301601 10.113271Â 0.22913929Â Â 2 15 > >Â Â Â Â Â Â positive regulation of cyclase activity > > > > I used GOstats for this analysis. If Count = 2, then shouldn't there > > be two genes that are directly annotated to this term? > > > > > > > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > > <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu>>> wrote: > > > > Hi Tim, > > > > There may not be any IDs mapped to that term directly. You can use > > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > >Â Â Â IDAÂ Â IDAÂ Â TASÂ Â TASÂ Â IDAÂ Â TAS IEA TAS TAS > > TAS > >Â Â "49"Â "116"Â "116"Â "117"Â "135"Â "135" "136" "136" "140" > > "153" > >Â Â Â IDAÂ Â IDAÂ Â TASÂ Â IDAÂ Â IEAÂ Â IDA IDA TAS IDA > > IEA > >Â Â "154"Â "155"Â "554"Â "796"Â "796"Â "799" "1394" "1394" "1812" > > "1812" > >Â Â Â IDAÂ Â IEAÂ Â NASÂ Â TASÂ Â TASÂ Â IEA TAS TAS IEA > > TAS > >Â "1816"Â "1816"Â "1816"Â "1816"Â "1909"Â "2692" "2696"Â "2740" "2774" > > "2778" > >Â Â Â IDAÂ Â ISSÂ Â ISSÂ Â IBAÂ Â IBAÂ Â IMP ISS TAS TAS > > TAS > >Â "2852"Â "3973"Â "4763"Â "4842"Â "4843"Â "4846" "4846"Â "4914" "4915" > > "5032" > >Â Â Â ISSÂ Â NASÂ Â IEAÂ Â IDAÂ Â IEAÂ Â TASÂ Â TAS > >Â "5578"Â "5894"Â "7077"Â "7432"Â "7434" "10486" "10487" > > > > Or the more powerful select() method: > > > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > >Â Â Â Â Â GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > > 1Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 49 ACR > > 2Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 116 ADCYAP1 > > 3Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 116 ADCYAP1 > > 4Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 117 ADCYAP1R1 > > 5Â GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 135 ADORA2A > > 6Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 135 ADORA2A > > 7Â GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 136 ADORA2B > > 8Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 136 ADORA2B > > 9Â GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 140 ADORA3 > > 10 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 153 ADRB1 > > 11 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 154 ADRB2 > > 12 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 155 ADRB3 > > 13 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â Â 554 AVPR2 > > 14 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 796 CALCA > > 15 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â Â 796 CALCA > > 16 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â Â 799 CALCR > > 17 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1394 CRHR1 > > 18 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1394 CRHR1 > > 19 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1812 DRD1 > > 20 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 1812 DRD1 > > 21 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 1816 DRD5 > > 22 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 1816 DRD5 > > 23 GO:0031281Â Â Â Â NASÂ Â Â Â Â BPÂ Â 1816 DRD5 > > 24 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1816 DRD5 > > 25 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 1909 EDNRA > > 26 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 2692 GHRHR > > 27 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2696 GIPR > > 28 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2740 GLP1R > > 29 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 2774 GNAL > > 30 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 2778 GNAS > > 31 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 2852 GPER1 > > 32 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 3973 LHCGR > > 33 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 4763 NF1 > > 34 GO:0031281Â Â Â Â IBAÂ Â Â Â Â BPÂ Â 4842 NOS1 > > 35 GO:0031281Â Â Â Â IBAÂ Â Â Â Â BPÂ Â 4843 NOS2 > > 36 GO:0031281Â Â Â Â IMPÂ Â Â Â Â BPÂ Â 4846 NOS3 > > 37 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 4846 NOS3 > > 38 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 4914 NTRK1 > > 39 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 4915 NTRK2 > > 40 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 5032 P2RY11 > > 41 GO:0031281Â Â Â Â ISSÂ Â Â Â Â BPÂ Â 5578 PRKCA > > 42 GO:0031281Â Â Â Â NASÂ Â Â Â Â BPÂ Â 5894 RAF1 > > 43 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 7077 TIMP2 > > 44 GO:0031281Â Â Â Â IDAÂ Â Â Â Â BPÂ Â 7432 VIP > > 45 GO:0031281Â Â Â Â IEAÂ Â Â Â Â BPÂ Â 7434 VIPR2 > > 46 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10486 CAP2 > > 47 GO:0031281Â Â Â Â TASÂ Â Â Â Â BPÂ Â 10487 CAP1 > > Warning message: > > In .generateExtraRows(tab, keys, jointype) : > >Â Â 'select' resulted in 1:many mapping between keys and return rows > > > > Best, > > > > Jim > > > > > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > > Hi, > > > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > > My code: > > > > > > library(org.Hs.eg.db) > > > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > > > When I run the code, I get: > > > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > > Error in .checkKeys(value, Rkeys(x), x@ifnotfound > <mailto:x@ifnotfound> > > <mailto:x@ifnotfound <mailto:x@ifnotfound="">>) : > > >Â Â value for "GO:0031281" not found > > > > > > If I check in AMIGO for this GO term, it seems to have many gene > > products for Homo sapiens. Am I doing something wrong? Is there an > > alternate package that I can try, just to double check the results? > > > > > > thanks! > > >Â Â [[alternative HTML version deleted]] > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org <mailto:bioconductor@r-project.org="">> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > >Â Â [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org <mailto:bioconductor@r-project.org="">> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

ADD REPLY • link 10.7 years ago Tim Smith ★ 1.1k

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Hi Tim, See ?probeSetSummary. As an example, after running the example for that function, you end up with a GOHyperGResults object called 'hyp': > head(summary(hyp)) GOBPID Pvalue OddsRatio ExpCount Count Size 1 GO:0031399 5.316815e-15 3.623932 28.94921 72 397 2 GO:0036211 2.482766e-14 2.949456 56.00249 107 768 3 GO:0023052 1.756878e-13 2.816284 110.47367 164 1515 And the first GO term has 72 significant genes out of 397 available. The 'ps' object is a list created by the probeSetSummary function, and each list item presents the Entrez Gene ID, Probeset ID, and an indicator showing it the probeset gave rise to the significant result (not really necessary - you could just use unique() on the EntrezID column if you wanted to): > head(ps[["GO:0031399"]]) EntrezID ProbeSetID selected 1 10114 102_at 1 2 10114 41501_at 0 3 10114 41502_at 0 4 10188 1134_at 1 And > sum(ps[["GO:0031399"]]$selected) [1] 72 Note that you either have to use a _named_ vector of geneIds when you set up your GOHyperGParams object > head(prbs) 1000_at 1001_at 1002_f_at 1003_s_at 1005_at 1006_at "5595" "7075" "1557" "643" "1843" "4319" as is done in that example, or you can pass in a set of IDs using the 'sigProbesets' argument to probeSetSummary(). Or you can just subset to the unique Entrez Gene IDs in whichever list item you are interested in. Best, Jim On 3/19/2014 5:17 PM, Tim Smith wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > > GOBPID Pvalue OddsRatio ExpCount Count Size > Term > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon at="" uw.edu=""> wrote: > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > IDA IDA TAS TAS IDA TAS IEA TAS TAS > TAS > "49" "116" "116" "117" "135" "135" "136" "136" "140" > "153" > IDA IDA TAS IDA IEA IDA IDA TAS IDA > IEA > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > "1812" > IDA IEA NAS TAS TAS IEA TAS TAS IEA > TAS > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > "2778" > IDA ISS ISS IBA IBA IMP ISS TAS TAS > TAS > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > "5032" > ISS NAS IEA IDA IEA TAS TAS > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1 GO:0031281 IDA BP 49 ACR > 2 GO:0031281 IDA BP 116 ADCYAP1 > 3 GO:0031281 TAS BP 116 ADCYAP1 > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > 5 GO:0031281 IDA BP 135 ADORA2A > 6 GO:0031281 TAS BP 135 ADORA2A > 7 GO:0031281 IEA BP 136 ADORA2B > 8 GO:0031281 TAS BP 136 ADORA2B > 9 GO:0031281 TAS BP 140 ADORA3 > 10 GO:0031281 TAS BP 153 ADRB1 > 11 GO:0031281 IDA BP 154 ADRB2 > 12 GO:0031281 IDA BP 155 ADRB3 > 13 GO:0031281 TAS BP 554 AVPR2 > 14 GO:0031281 IDA BP 796 CALCA > 15 GO:0031281 IEA BP 796 CALCA > 16 GO:0031281 IDA BP 799 CALCR > 17 GO:0031281 IDA BP 1394 CRHR1 > 18 GO:0031281 TAS BP 1394 CRHR1 > 19 GO:0031281 IDA BP 1812 DRD1 > 20 GO:0031281 IEA BP 1812 DRD1 > 21 GO:0031281 IDA BP 1816 DRD5 > 22 GO:0031281 IEA BP 1816 DRD5 > 23 GO:0031281 NAS BP 1816 DRD5 > 24 GO:0031281 TAS BP 1816 DRD5 > 25 GO:0031281 TAS BP 1909 EDNRA > 26 GO:0031281 IEA BP 2692 GHRHR > 27 GO:0031281 TAS BP 2696 GIPR > 28 GO:0031281 TAS BP 2740 GLP1R > 29 GO:0031281 IEA BP 2774 GNAL > 30 GO:0031281 TAS BP 2778 GNAS > 31 GO:0031281 IDA BP 2852 GPER1 > 32 GO:0031281 ISS BP 3973 LHCGR > 33 GO:0031281 ISS BP 4763 NF1 > 34 GO:0031281 IBA BP 4842 NOS1 > 35 GO:0031281 IBA BP 4843 NOS2 > 36 GO:0031281 IMP BP 4846 NOS3 > 37 GO:0031281 ISS BP 4846 NOS3 > 38 GO:0031281 TAS BP 4914 NTRK1 > 39 GO:0031281 TAS BP 4915 NTRK2 > 40 GO:0031281 TAS BP 5032 P2RY11 > 41 GO:0031281 ISS BP 5578 PRKCA > 42 GO:0031281 NAS BP 5894 RAF1 > 43 GO:0031281 IEA BP 7077 TIMP2 > 44 GO:0031281 IDA BP 7432 VIP > 45 GO:0031281 IEA BP 7434 VIPR2 > 46 GO:0031281 TAS BP 10486 CAP2 > 47 GO:0031281 TAS BP 10487 CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : > 'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound="">) : > > value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

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