cateGOry error

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Oleg Sklyar ▴ 260

@oleg-sklyar-1882

Last seen 10.2 years ago

Hi, I am having troubles with cateGOry as follows: > m <- cateGOry(go$refseq_dna, go$go, FALSE) Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 were mentioned in 'x' but were not found in the GO package. what this error means was not clear, so I tried those as indexes in my data, as follows first, or as GO ids as follows second. Neither worked. Any idea? Thanks, Oleg > index <- c(24, 172, 1978, 1979, 4441) > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 were mentioned in 'x' but were not found in the GO package. > terms <- c("GO:0000024", "GO:0000172", "GO:0001978", "GO:0001979", "GO:0004442") > index <- which(go$go %in% terms) > go$go[index] [1] "GO:0000172" "GO:0000172" > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4441 were mentioned in 'x' but were not found in the GO package. -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466

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ADD COMMENT • link updated 17.5 years ago by Wolfgang Huber ★ 13k • written 17.5 years ago by Oleg Sklyar ▴ 260

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.2 years ago

Oleg Sklyar <osklyar at="" ebi.ac.uk=""> writes: > Hi, > > I am having troubles with cateGOry as follows: > > > m <- cateGOry(go$refseq_dna, go$go, FALSE) > Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 > were mentioned in 'x' but were not found in the GO package. > > what this error means was not clear, so I tried those as indexes in my > data, as follows first, or as GO ids as follows second. Neither worked. > Any idea? Thanks, Oleg What is typeof(go$go)? Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it looks like these valus should be GO IDs (element of the categ argument to cateGOry). Are you sure those values are not in go$go? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

ADD COMMENT • link 17.5 years ago Seth Falcon ★ 7.4k

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> Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it > looks like these valus should be GO IDs (element of the categ argument > to cateGOry). Are you sure those values are not in go$go? I did the grep and at least the 0024 does not appear there at all. By using %in% I find only 172. But I have further problems, like the following and starting to suspect that something is wrong with character operations: > class(entrez) [1] "character" > entrez[120000:120010] [1] NA NA NA NA NA NA NA NA NA NA NA > whichis.na(entrez)) integer(0) > which(entrez=="NA") integer(0) How can I get onto those NA's? > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: Category Matrix lattice genefilter survival annotate "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" GO KEGG graph Biobase biomaRt RCurl "1.16.0" "1.16.0" "1.14.0" "1.14.0" "1.10.0" "0.8-0" XML "1.9-0"

ADD REPLY • link 17.5 years ago Oleg Sklyar ▴ 260

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Oleg Sklyar wrote: >>Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it >>looks like these valus should be GO IDs (element of the categ argument >>to cateGOry). Are you sure those values are not in go$go? > > I did the grep and at least the 0024 does not appear there at all. By > using %in% I find only 172. But I have further problems, like the > following and starting to suspect that something is wrong with character > operations: > > > class(entrez) > [1] "character" > > entrez[120000:120010] > [1] NA NA NA NA NA NA NA NA NA NA NA Is your entrez vector really that long? Any subsetting operation off the end of a vector will return NAs. Best, Jim > > whichis.na(entrez)) > integer(0) > > which(entrez=="NA") > integer(0) > > How can I get onto those NA's? > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_G B.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > Category Matrix lattice genefilter survival annotate > "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" > GO KEGG graph Biobase biomaRt RCurl > "1.16.0" "1.16.0" "1.14.0" "1.14.0" "1.10.0" "0.8-0" > XML > "1.9-0" > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 17.5 years ago James W. MacDonald 67k

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Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 3 months ago

EMBL European Molecular Biology Laborat…

Dear Oleg, please use a more recent version of cateGOry, where I have fixed the error message to be more meaningful. It means that you are supplying GO categories for which there is no information in the Bioconductor GO package, either because they have been retired or because they have been created after the package was made. See also: https://stat.ethz.ch/pipermail/bioc-devel/2007-May/001108.html Regarding your NA problem, as Jim already pointed out, isn't this equivalent to a="gaga" a[2] [1] NA Best wishes Wolfgang Sklyar ha scritto: > Hi, > > I am having troubles with cateGOry as follows: > > > m <- cateGOry(go$refseq_dna, go$go, FALSE) > Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 > were mentioned in 'x' but were not found in the GO package. > > what this error means was not clear, so I tried those as indexes in my > data, as follows first, or as GO ids as follows second. Neither worked. > Any idea? Thanks, Oleg > > > index <- c(24, 172, 1978, 1979, 4441) > > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) > Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 > were mentioned in 'x' but were not found in the GO package. > > > terms <- c("GO:0000024", "GO:0000172", "GO:0001978", "GO:0001979", > "GO:0004442") > > index <- which(go$go %in% terms) > > go$go[index] > [1] "GO:0000172" "GO:0000172" > > > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) > Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4441 > were mentioned in 'x' but were not found in the GO package. > -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

ADD COMMENT • link 17.5 years ago Wolfgang Huber ★ 13k

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