problem with probes2tableBM
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@mayte-suarez-farinas-2068
Last seen 9.5 years ago
United States
Hi, I am having problems with function probes2tableBM again, and I can not figure it out what is the right ann.source for hgu133a2 chips. here is the code > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > probes2tableBM(eset, probids=featureNames(eset) [1:10],filename='llll', + species="hsapiens", ann.source="affy_hg_u133a_2", links=linksBM()[c(1:3)], otherann=annBM ()[1:2], affyid=TRUE, express=FALSE) connected to: ensembl Reading database configuration of: hsapiens_gene_ensembl Checking attributes and filters ... ok Checking main tables ... ok Error in getBM(attributes = links$links, filter = ann.source, values = gn, : Invalid attribute(s): affy_hg_u133a_2 Please use the function 'listAttributes' to get valid attribute names when I do that: > listAttributes(mart_hs)[1:20,] name description 1 affy_hcg110 AFFY HCG110 2 affy_hg_focus AFFY HG FOCUS 3 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 4 affy_hg_u133a AFFY HG U133A 5 affy_hg_u133a_v2 AFFY HG U133Av2 6 affy_hg_u133b AFFY HG U133B 7 affy_hg_u95a AFFY HG U95A 8 affy_hg_u95av2 AFFY HG U95AV2 9 affy_hg_u95b AFFY HG U95B 10 affy_hg_u95c AFFY HG U95C 11 affy_hg_u95d AFFY HG U95D 12 affy_hg_u95e AFFY HG U95E 13 affy_hugenefl AFFY HUGENEFL 14 affy_u133_x3p AFFY U133 X3P 15 agilent_cgh Agilent cgh 16 agilent_probe Agilent Probe 17 band Band 18 biotype Biotype 19 ccds CCDS ID 20 chromosome_name Chromosome Name so I tried with ann.source=affy_hg_u133a_v2 but I get another error: > probes2tableBM(eset, probids=featureNames(eset) [1:10],filename='llll', + species="hsapiens", ann.source="affy_hg_u133a_v2", links=linksBM()[c(1:3)], otherann=annBM ()[1:2], affyid=TRUE, express=FALSE) connected to: ensembl Reading database configuration of: hsapiens_gene_ensembl Checking attributes and filters ... ok Checking main tables ... ok Error: ' affy_hg_u133a_v2 'is not an available annotation source for this biomaRt or this species. Available choices are listed below: name description 1 affy_hc_g110 Affy hc g 110 ID(s) 2 affy_hg_focus Affy hg focus ID(s) 3 affy_hg_u133_plus_2 Affy hg u133 plus 2 ID(s) 4 affy_hg_u133a Affy hg u133a ID(s) 5 affy_hg_u133a_2 Affy hg u133a 2 ID(s) 6 affy_hg_u133b Affy hg u133b ID(s) 7 affy_hg_u95a Affy hg u95a ID(s) 8 affy_hg_u95av2 Affy hg u95av2 ID(s) 9 affy_hg_u95b Affy hg u95b ID(s) 10 affy_hg_u95c Affy hg u95c ID(s) 11 affy_hg_u95d Affy hg u95d ID(s) 12 affy_hg_u95e Affy hg u95e ID(s) 13 affy_hugenefl Affy hugenefl ID(s) 14 affy_u133_x3p Affy u133 x3p ID(s) ............ sessionInfo() R version 2.5.0 (2007-04-23) i386-apple-darwin8.9.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: RMySQL DBI affycoretools annaffy xtable gcrma matchprobes biomaRt RCurl "0.5-11" "0.2-2" "1.8.0" "1.8.1" "1.4-3" "2.8.0" "1.8.1" "1.10.0" "0.8-0" XML GOstats Category Matrix lattice genefilter survival KEGG RBGL "1.7-3" "2.2.1" "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.15.13" "1.12.0" annotate GO graph limma affy affyio Biobase "1.14.1" "1.16.0" "1.14.0" "2.10.0" "1.14.0" "1.4.0" "1.14.0"
Annotation GO Survival hgu133a2 annotate genefilter affy graph gcrma matchprobes GOstats • 1.4k views
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Steffen ▴ 500
@steffen-2351
Last seen 10.2 years ago
Hi Mayte, The hgu133a2 chip has a different attribute and filter name in Ensembl and it looks like the probes2tableBM function assumes that the filter and attribute names are the same for every platform (ideally it should). The attribute name for this platform is affy_hg_u133a_v2 and the filter name is affy_hg_u133a_2. Maybe Jim can comment on how to get the function working in this case? Alternatively you can do your query using the getBM function instead of probes2tableBM. Cheers, Steffen Mayte Suarez-Farinas wrote: > Hi, > > I am having problems with function probes2tableBM again, and I can > not figure it out what is the right > ann.source for hgu133a2 chips. here is the code > > > > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") > Checking attributes and filters ... ok > > > probes2tableBM(eset, probids=featureNames(eset) > [1:10],filename='llll', > + species="hsapiens", > ann.source="affy_hg_u133a_2", links=linksBM()[c(1:3)], otherann=annBM > ()[1:2], affyid=TRUE, express=FALSE) > connected to: ensembl > Reading database configuration of: hsapiens_gene_ensembl > Checking attributes and filters ... ok > Checking main tables ... ok > Error in getBM(attributes = links$links, filter = ann.source, values > = gn, : > Invalid attribute(s): affy_hg_u133a_2 > Please use the function 'listAttributes' to get valid attribute names > > > when I do that: > > > listAttributes(mart_hs)[1:20,] > name description > 1 affy_hcg110 AFFY HCG110 > 2 affy_hg_focus AFFY HG FOCUS > 3 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 > 4 affy_hg_u133a AFFY HG U133A > 5 affy_hg_u133a_v2 AFFY HG U133Av2 > 6 affy_hg_u133b AFFY HG U133B > 7 affy_hg_u95a AFFY HG U95A > 8 affy_hg_u95av2 AFFY HG U95AV2 > 9 affy_hg_u95b AFFY HG U95B > 10 affy_hg_u95c AFFY HG U95C > 11 affy_hg_u95d AFFY HG U95D > 12 affy_hg_u95e AFFY HG U95E > 13 affy_hugenefl AFFY HUGENEFL > 14 affy_u133_x3p AFFY U133 X3P > 15 agilent_cgh Agilent cgh > 16 agilent_probe Agilent Probe > 17 band Band > 18 biotype Biotype > 19 ccds CCDS ID > 20 chromosome_name Chromosome Name > > > > so I tried with ann.source=affy_hg_u133a_v2 but I get another error: > > > probes2tableBM(eset, probids=featureNames(eset) > [1:10],filename='llll', > + species="hsapiens", > ann.source="affy_hg_u133a_v2", links=linksBM()[c(1:3)], otherann=annBM > ()[1:2], affyid=TRUE, express=FALSE) > connected to: ensembl > Reading database configuration of: hsapiens_gene_ensembl > Checking attributes and filters ... ok > Checking main tables ... ok > Error: ' affy_hg_u133a_v2 'is not an available annotation source for > this biomaRt or this species. > Available choices are listed below: > name > description > 1 affy_hc_g110 Affy hc g 110 > ID(s) > 2 affy_hg_focus Affy hg focus > ID(s) > 3 affy_hg_u133_plus_2 Affy hg u133 plus 2 > ID(s) > 4 affy_hg_u133a Affy hg u133a > ID(s) > 5 affy_hg_u133a_2 Affy hg u133a 2 > ID(s) > 6 affy_hg_u133b Affy hg u133b > ID(s) > 7 affy_hg_u95a Affy hg u95a > ID(s) > 8 affy_hg_u95av2 Affy hg u95av2 > ID(s) > 9 affy_hg_u95b Affy hg u95b > ID(s) > 10 affy_hg_u95c Affy hg u95c > ID(s) > 11 affy_hg_u95d Affy hg u95d > ID(s) > 12 affy_hg_u95e Affy hg u95e > ID(s) > 13 affy_hugenefl Affy hugenefl > ID(s) > 14 affy_u133_x3p Affy u133 x3p > ID(s) > ............ > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > i386-apple-darwin8.9.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" > "utils" "datasets" "methods" "base" > > other attached packages: > RMySQL DBI affycoretools annaffy > xtable gcrma matchprobes biomaRt RCurl > "0.5-11" "0.2-2" "1.8.0" "1.8.1" > "1.4-3" "2.8.0" "1.8.1" "1.10.0" "0.8-0" > XML GOstats Category Matrix > lattice genefilter survival KEGG RBGL > "1.7-3" "2.2.1" "2.2.1" "0.9975-11" > "0.15-4" "1.14.1" "2.31" "1.15.13" "1.12.0" > annotate GO graph limma > affy affyio Biobase > "1.14.1" "1.16.0" "1.14.0" "2.10.0" > "1.14.0" "1.4.0" "1.14.0" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Hi Mayte, You have uncovered a bug in probes2tableBM(). I will fix this in the devel version. I am in the process of setting up a new work computer, so I am not able to check things out right now - when I am able I will see if there is a quick workaround that will get you going right now. Best, Jim Steffen wrote: > Hi Mayte, > > The hgu133a2 chip has a different attribute and filter name in Ensembl > and it looks like the probes2tableBM function assumes that the filter > and attribute names are the same for every platform (ideally it should). > The attribute name for this platform is affy_hg_u133a_v2 and the filter > name is affy_hg_u133a_2. Maybe Jim can comment on how to get the > function working in this case? > Alternatively you can do your query using the getBM function instead of > probes2tableBM. > > Cheers, > Steffen > > > Mayte Suarez-Farinas wrote: >> Hi, >> >> I am having problems with function probes2tableBM again, and I can >> not figure it out what is the right >> ann.source for hgu133a2 chips. here is the code >> >> >> > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> Checking attributes and filters ... ok >> >> > probes2tableBM(eset, probids=featureNames(eset) >> [1:10],filename='llll', >> + species="hsapiens", >> ann.source="affy_hg_u133a_2", links=linksBM()[c(1:3)], otherann=annBM >> ()[1:2], affyid=TRUE, express=FALSE) >> connected to: ensembl >> Reading database configuration of: hsapiens_gene_ensembl >> Checking attributes and filters ... ok >> Checking main tables ... ok >> Error in getBM(attributes = links$links, filter = ann.source, values >> = gn, : >> Invalid attribute(s): affy_hg_u133a_2 >> Please use the function 'listAttributes' to get valid attribute names >> >> >> when I do that: >> >> > listAttributes(mart_hs)[1:20,] >> name description >> 1 affy_hcg110 AFFY HCG110 >> 2 affy_hg_focus AFFY HG FOCUS >> 3 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 >> 4 affy_hg_u133a AFFY HG U133A >> 5 affy_hg_u133a_v2 AFFY HG U133Av2 >> 6 affy_hg_u133b AFFY HG U133B >> 7 affy_hg_u95a AFFY HG U95A >> 8 affy_hg_u95av2 AFFY HG U95AV2 >> 9 affy_hg_u95b AFFY HG U95B >> 10 affy_hg_u95c AFFY HG U95C >> 11 affy_hg_u95d AFFY HG U95D >> 12 affy_hg_u95e AFFY HG U95E >> 13 affy_hugenefl AFFY HUGENEFL >> 14 affy_u133_x3p AFFY U133 X3P >> 15 agilent_cgh Agilent cgh >> 16 agilent_probe Agilent Probe >> 17 band Band >> 18 biotype Biotype >> 19 ccds CCDS ID >> 20 chromosome_name Chromosome Name >> >> >> >> so I tried with ann.source=affy_hg_u133a_v2 but I get another error: >> >> > probes2tableBM(eset, probids=featureNames(eset) >> [1:10],filename='llll', >> + species="hsapiens", >> ann.source="affy_hg_u133a_v2", links=linksBM()[c(1:3)], otherann=annBM >> ()[1:2], affyid=TRUE, express=FALSE) >> connected to: ensembl >> Reading database configuration of: hsapiens_gene_ensembl >> Checking attributes and filters ... ok >> Checking main tables ... ok >> Error: ' affy_hg_u133a_v2 'is not an available annotation source for >> this biomaRt or this species. >> Available choices are listed below: >> name >> description >> 1 affy_hc_g110 Affy hc g 110 >> ID(s) >> 2 affy_hg_focus Affy hg focus >> ID(s) >> 3 affy_hg_u133_plus_2 Affy hg u133 plus 2 >> ID(s) >> 4 affy_hg_u133a Affy hg u133a >> ID(s) >> 5 affy_hg_u133a_2 Affy hg u133a 2 >> ID(s) >> 6 affy_hg_u133b Affy hg u133b >> ID(s) >> 7 affy_hg_u95a Affy hg u95a >> ID(s) >> 8 affy_hg_u95av2 Affy hg u95av2 >> ID(s) >> 9 affy_hg_u95b Affy hg u95b >> ID(s) >> 10 affy_hg_u95c Affy hg u95c >> ID(s) >> 11 affy_hg_u95d Affy hg u95d >> ID(s) >> 12 affy_hg_u95e Affy hg u95e >> ID(s) >> 13 affy_hugenefl Affy hugenefl >> ID(s) >> 14 affy_u133_x3p Affy u133 x3p >> ID(s) >> ............ >> >> >> >> sessionInfo() >> R version 2.5.0 (2007-04-23) >> i386-apple-darwin8.9.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" "datasets" "methods" "base" >> >> other attached packages: >> RMySQL DBI affycoretools annaffy >> xtable gcrma matchprobes biomaRt RCurl >> "0.5-11" "0.2-2" "1.8.0" "1.8.1" >> "1.4-3" "2.8.0" "1.8.1" "1.10.0" "0.8-0" >> XML GOstats Category Matrix >> lattice genefilter survival KEGG RBGL >> "1.7-3" "2.2.1" "2.2.1" "0.9975-11" >> "0.15-4" "1.14.1" "2.31" "1.15.13" "1.12.0" >> annotate GO graph limma >> affy affyio Biobase >> "1.14.1" "1.16.0" "1.14.0" "2.10.0" >> "1.14.0" "1.4.0" "1.14.0" >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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