Bug in getOntoly-function (package annotate)?
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Jukka Hiissa ▴ 20
@jukka-hiissa-3051
Last seen 10.3 years ago
Dear BioC users, I am having problems with the getOntology-function (annotate-package v. 1.18 ) The command getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" ) [1] "GO:0032515" "GO:0032516" returns two GO identifiers, but they are not correct since their ontologies are in fact NA $`GO:0032515` $`GO:0032515`$GOID [1] "GO:0032515" $`GO:0032515`$Evidence [1] "IDA" $`GO:0032515`$Ontology [1] NA $`GO:0032516` $`GO:0032516`$GOID [1] "GO:0032516" $`GO:0032516`$Evidence [1] "IDA" $`GO:0032516`$Ontology [1] NA I looked at the getOntology source code and I think that the problem is that the NAs are removed from the index vector but not from the list containing the GO-elements. The last two lines in the getOntology function are onts = onts[!is.na(onts)] unique(names(inlist[onts %in% which])) where the onts contains the ontology labels, e.g. GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601 NA "MF" "CC" "MF" "MF" "MF" GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308 "MF" "MF" NA NA "BP" "BP" GO:0042803 GO:0046982 GO:0051721 "MF" "MF" "MF" After the NAs are removed from the onts vector the indexes of the two BP-ontology cases are 8 and 9, but these are not the correct indexes for the inlist list, which still contains the three missing ontology cases. names( inlist ) [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601" [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516" [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721 Best regards, Jukka Hiissa
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
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Hi Jukka, Can you please give us the results of calling sessionInfo()? From what I can see below it looks like you are using a custom annotation package. Is that correct? Marc Jukka Hiissa wrote: > Dear BioC users, > > I am having problems with the getOntology-function (annotate-package v. > 1.18 ) The command > > getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" ) > [1] "GO:0032515" "GO:0032516" > > returns two GO identifiers, but they are not correct since their > ontologies are in fact NA > > $`GO:0032515` > $`GO:0032515`$GOID > [1] "GO:0032515" > $`GO:0032515`$Evidence > [1] "IDA" > $`GO:0032515`$Ontology > [1] NA > > $`GO:0032516` > $`GO:0032516`$GOID > [1] "GO:0032516" > $`GO:0032516`$Evidence > [1] "IDA" > $`GO:0032516`$Ontology > [1] NA > > I looked at the getOntology source code and I think that the problem is > that the NAs are removed from the index vector but not from the list > containing the GO-elements. The last two lines in the getOntology > function are > > onts = onts[!is.na(onts)] > unique(names(inlist[onts %in% which])) > > where the onts contains the ontology labels, e.g. > > GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601 > NA "MF" "CC" "MF" "MF" "MF" > GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308 > "MF" "MF" NA NA "BP" "BP" > GO:0042803 GO:0046982 GO:0051721 > "MF" "MF" "MF" > > After the NAs are removed from the onts vector the indexes of the two > BP-ontology cases are 8 and 9, but these are not the correct indexes for > the inlist list, which still contains the three missing ontology cases. > > names( inlist ) > [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601" > [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516" > [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721 > > Best regards, > Jukka Hiissa > > _______________________________________________ > 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 Marc and thanks for the fast reply. That is correct, I am using a custom-made annotation package. I have attached the list returned by the command getGO( "7650504", "illuminaHumanBCv2")[[1]] at the end of my message. Here is my sessionInfo: > sessionInfo() R version 2.6.1 (2007-11-26) i486-pc-linux-gnu locale: LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = en_US .UTF -8 ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] illuminaHumanBCv2_08.08.07 annotate_1.18.0 [3] xtable_1.5-2 AnnotationDbi_1.0.6 [5] RSQLite_0.6-7 DBI_0.2-4 [7] Biobase_1.16.2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 > I know that my R and BioC are slightly old, but I will upgrade them (and also my Ubuntu 7.10) as soon as I have finished my current analysis, hopely within a few weeks. The version of the annotate package was originally 1.16.1 but I upgraded it manually, just in case. By the way, I commented the line "onts = onts[!is.na(onts)]" in the getOntology-function and now it seems to work. Best regards, Jukka > getGO("7650504", "illuminaHumanBCv2")[[1]] $`GO:0000159` $`GO:0000159`$GOID [1] "GO:0000159" $`GO:0000159`$Evidence [1] "TAS" $`GO:0000159`$Ontology [1] "CC" $`GO:0005524` $`GO:0005524`$GOID [1] "GO:0005524" $`GO:0005524`$Evidence [1] "IDA" $`GO:0005524`$Ontology [1] "MF" $`GO:0005625` $`GO:0005625`$GOID [1] "GO:0005625" $`GO:0005625`$Evidence [1] "TAS" $`GO:0005625`$Ontology [1] "CC" $`GO:0008160` $`GO:0008160`$GOID [1] "GO:0008160" $`GO:0008160`$Evidence [1] "IDA" $`GO:0008160`$Ontology [1] "MF" $`GO:0008601` $`GO:0008601`$GOID [1] "GO:0008601" $`GO:0008601`$Evidence [1] "IDA" $`GO:0008601`$Ontology [1] "MF" $`GO:0008601` $`GO:0008601`$GOID [1] "GO:0008601" $`GO:0008601`$Evidence [1] "TAS" $`GO:0008601`$Ontology [1] "MF" $`GO:0016887` $`GO:0016887`$GOID [1] "GO:0016887" $`GO:0016887`$Evidence [1] "IDA" $`GO:0016887`$Ontology [1] "MF" $`GO:0019211` $`GO:0019211`$GOID [1] "GO:0019211" $`GO:0019211`$Evidence [1] "IEA" $`GO:0019211`$Ontology [1] "MF" $`GO:0032515` $`GO:0032515`$GOID [1] "GO:0032515" $`GO:0032515`$Evidence [1] "IDA" $`GO:0032515`$Ontology [1] NA $`GO:0032516` $`GO:0032516`$GOID [1] "GO:0032516" $`GO:0032516`$Evidence [1] "IDA" $`GO:0032516`$Ontology [1] NA $`GO:0035307` $`GO:0035307`$GOID [1] "GO:0035307" $`GO:0035307`$Evidence [1] "IDA" $`GO:0035307`$Ontology [1] "BP" $`GO:0035308` $`GO:0035308`$GOID [1] "GO:0035308" $`GO:0035308`$Evidence [1] "IDA" $`GO:0035308`$Ontology [1] "BP" $`GO:0042803` $`GO:0042803`$GOID [1] "GO:0042803" $`GO:0042803`$Evidence [1] "IDA" $`GO:0042803`$Ontology [1] "MF" $`GO:0046982` $`GO:0046982`$GOID [1] "GO:0046982" $`GO:0046982`$Evidence [1] "TAS" $`GO:0046982`$Ontology [1] "MF" $`GO:0051721` $`GO:0051721`$GOID [1] "GO:0051721" $`GO:0051721`$Evidence [1] "IDA" $`GO:0051721`$Ontology [1] "MF" > Marc Carlson kirjoitti 2.10.2008 kello 19.59: > Hi Jukka, > > Can you please give us the results of calling sessionInfo()? From > what > I can see below it looks like you are using a custom annotation > package. Is that correct? > > Marc > > > > > Jukka Hiissa wrote: >> Dear BioC users, >> >> I am having problems with the getOntology-function (annotate- >> package v. >> 1.18 ) The command >> >> getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" ) >> [1] "GO:0032515" "GO:0032516" >> >> returns two GO identifiers, but they are not correct since their >> ontologies are in fact NA >> >> $`GO:0032515` >> $`GO:0032515`$GOID >> [1] "GO:0032515" >> $`GO:0032515`$Evidence >> [1] "IDA" >> $`GO:0032515`$Ontology >> [1] NA >> >> $`GO:0032516` >> $`GO:0032516`$GOID >> [1] "GO:0032516" >> $`GO:0032516`$Evidence >> [1] "IDA" >> $`GO:0032516`$Ontology >> [1] NA >> >> I looked at the getOntology source code and I think that the >> problem is >> that the NAs are removed from the index vector but not from the list >> containing the GO-elements. The last two lines in the getOntology >> function are >> >> onts = onts[!is.na(onts)] >> unique(names(inlist[onts %in% which])) >> >> where the onts contains the ontology labels, e.g. >> >> GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601 >> NA "MF" "CC" "MF" "MF" "MF" >> GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308 >> "MF" "MF" NA NA "BP" "BP" >> GO:0042803 GO:0046982 GO:0051721 >> "MF" "MF" "MF" >> >> After the NAs are removed from the onts vector the indexes of the two >> BP-ontology cases are 8 and 9, but these are not the correct >> indexes for >> the inlist list, which still contains the three missing ontology >> cases. >> >> names( inlist ) >> [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601" >> [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516" >> [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721 >> >> Best regards, >> Jukka Hiissa >> >> _______________________________________________ >> 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 Jukka, The annotation package you are using really should be updated. The current version is illuminaHumanv2ProbeID.db and as the name indicates uses the Probe ID as the identifier as was used in illuminaHumanBCv2. Please use this new package. Lynn Jukka Hiissa wrote: > Hi Marc and thanks for the fast reply. > > That is correct, I am using a custom-made annotation package. I have > attached the list returned by the command getGO( "7650504", > "illuminaHumanBCv2")[[1]] at the end of my message. > > Here is my sessionInfo: > > > sessionInfo() > R version 2.6.1 (2007-11-26) > i486-pc-linux-gnu > > locale: > LC_CTYPE > = > en_US > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_US > .UTF > -8 > ;LC_COLLATE > = > en_US > .UTF > -8 > ;LC_MONETARY > = > en_US > .UTF > -8 > ;LC_MESSAGES > = > en_US > .UTF > -8 > ;LC_PAPER > = > en_US > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] illuminaHumanBCv2_08.08.07 annotate_1.18.0 > [3] xtable_1.5-2 AnnotationDbi_1.0.6 > [5] RSQLite_0.6-7 DBI_0.2-4 > [7] Biobase_1.16.2 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 > > > > I know that my R and BioC are slightly old, but I will upgrade them > (and also my Ubuntu 7.10) as soon as I have finished my current > analysis, hopely within a few weeks. The version of the annotate > package was originally 1.16.1 but I upgraded it manually, just in > case. > > By the way, I commented the line "onts = onts[!is.na(onts)]" in the > getOntology-function and now it seems to work. > > Best regards, > Jukka > > > > getGO("7650504", "illuminaHumanBCv2")[[1]] > $`GO:0000159` > $`GO:0000159`$GOID > [1] "GO:0000159" > > $`GO:0000159`$Evidence > [1] "TAS" > > $`GO:0000159`$Ontology > [1] "CC" > > $`GO:0005524` > $`GO:0005524`$GOID > [1] "GO:0005524" > > $`GO:0005524`$Evidence > [1] "IDA" > > $`GO:0005524`$Ontology > [1] "MF" > > $`GO:0005625` > $`GO:0005625`$GOID > [1] "GO:0005625" > > $`GO:0005625`$Evidence > [1] "TAS" > > $`GO:0005625`$Ontology > [1] "CC" > > $`GO:0008160` > $`GO:0008160`$GOID > [1] "GO:0008160" > > $`GO:0008160`$Evidence > [1] "IDA" > > $`GO:0008160`$Ontology > [1] "MF" > > $`GO:0008601` > $`GO:0008601`$GOID > [1] "GO:0008601" > > $`GO:0008601`$Evidence > [1] "IDA" > > $`GO:0008601`$Ontology > [1] "MF" > > $`GO:0008601` > $`GO:0008601`$GOID > [1] "GO:0008601" > > $`GO:0008601`$Evidence > [1] "TAS" > > $`GO:0008601`$Ontology > [1] "MF" > > $`GO:0016887` > $`GO:0016887`$GOID > [1] "GO:0016887" > > $`GO:0016887`$Evidence > [1] "IDA" > > $`GO:0016887`$Ontology > [1] "MF" > > $`GO:0019211` > $`GO:0019211`$GOID > [1] "GO:0019211" > > $`GO:0019211`$Evidence > [1] "IEA" > > $`GO:0019211`$Ontology > [1] "MF" > > $`GO:0032515` > $`GO:0032515`$GOID > [1] "GO:0032515" > > $`GO:0032515`$Evidence > [1] "IDA" > > $`GO:0032515`$Ontology > [1] NA > > $`GO:0032516` > $`GO:0032516`$GOID > [1] "GO:0032516" > > $`GO:0032516`$Evidence > [1] "IDA" > > $`GO:0032516`$Ontology > [1] NA > > $`GO:0035307` > $`GO:0035307`$GOID > [1] "GO:0035307" > > $`GO:0035307`$Evidence > [1] "IDA" > > $`GO:0035307`$Ontology > [1] "BP" > > $`GO:0035308` > $`GO:0035308`$GOID > [1] "GO:0035308" > > $`GO:0035308`$Evidence > [1] "IDA" > > $`GO:0035308`$Ontology > [1] "BP" > > $`GO:0042803` > $`GO:0042803`$GOID > [1] "GO:0042803" > > $`GO:0042803`$Evidence > [1] "IDA" > > $`GO:0042803`$Ontology > [1] "MF" > > $`GO:0046982` > $`GO:0046982`$GOID > [1] "GO:0046982" > > $`GO:0046982`$Evidence > [1] "TAS" > > $`GO:0046982`$Ontology > [1] "MF" > > $`GO:0051721` > $`GO:0051721`$GOID > [1] "GO:0051721" > > $`GO:0051721`$Evidence > [1] "IDA" > > $`GO:0051721`$Ontology > [1] "MF" > > > > > Marc Carlson kirjoitti 2.10.2008 kello 19.59: > >> Hi Jukka, >> >> Can you please give us the results of calling sessionInfo()? From what >> I can see below it looks like you are using a custom annotation >> package. Is that correct? >> >> Marc >> >> >> >> >> Jukka Hiissa wrote: >>> Dear BioC users, >>> >>> I am having problems with the getOntology-function (annotate- package v. >>> 1.18 ) The command >>> >>> getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" ) >>> [1] "GO:0032515" "GO:0032516" >>> >>> returns two GO identifiers, but they are not correct since their >>> ontologies are in fact NA >>> >>> $`GO:0032515` >>> $`GO:0032515`$GOID >>> [1] "GO:0032515" >>> $`GO:0032515`$Evidence >>> [1] "IDA" >>> $`GO:0032515`$Ontology >>> [1] NA >>> >>> $`GO:0032516` >>> $`GO:0032516`$GOID >>> [1] "GO:0032516" >>> $`GO:0032516`$Evidence >>> [1] "IDA" >>> $`GO:0032516`$Ontology >>> [1] NA >>> >>> I looked at the getOntology source code and I think that the problem is >>> that the NAs are removed from the index vector but not from the list >>> containing the GO-elements. The last two lines in the getOntology >>> function are >>> >>> onts = onts[!is.na(onts)] >>> unique(names(inlist[onts %in% which])) >>> >>> where the onts contains the ontology labels, e.g. >>> >>> GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601 >>> NA "MF" "CC" "MF" "MF" "MF" >>> GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308 >>> "MF" "MF" NA NA "BP" "BP" >>> GO:0042803 GO:0046982 GO:0051721 >>> "MF" "MF" "MF" >>> >>> After the NAs are removed from the onts vector the indexes of the two >>> BP-ontology cases are 8 and 9, but these are not the correct indexes >>> for >>> the inlist list, which still contains the three missing ontology cases. >>> >>> names( inlist ) >>> [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601" >>> [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516" >>> [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721 >>> >>> Best regards, >>> Jukka Hiissa >>> >>> _______________________________________________ >>> 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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