Hello, With the help of this list I succeeded in creating an annotation package using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which installs fine. I then tried to run goTools' ontoCompare function like this: result <- ontoCompare(ProtNames, probeType = "Mus.musculus.GoMap.20070223") After a LONG time, it stops with the following: Error in as.vector(x, mode) : invalid argument 'mode' error Does anyone spot what I'm doing wrong? Thanks, Joh

try another package for GO testing? and setting options(error=recover) will put you into the debugger from where you might be able to figure out what went wrong, and at least it will give you (and us) some ideas. Also, please read the posting guide and provide the information it tells you is needed (and indeed is needed) for someone to be able to help you Johannes Graumann wrote: > Hello, > > With the help of this list I succeeded in creating an annotation package > using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which > installs fine. > I then tried to run goTools' ontoCompare function like this: > > result <- ontoCompare(ProtNames, probeType = "Mus.musculus.GoMap.20070223") > > After a LONG time, it stops with the following: > Error in as.vector(x, mode) : invalid argument 'mode' error > > Does anyone spot what I'm doing wrong? > > Thanks, Joh > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi Johannes, OntoCompare will only work with the following probe types: Gene Ontology ids, Affymetrix oligo Ids and Operon human and Mouse oligo ids. Other types will not be recognized and you will get an error. Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Johannes Graumann Sent: Fri 2/23/2007 8:05 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] OntoCompare Error Hello, With the help of this list I succeeded in creating an annotation package using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which installs fine. I then tried to run goTools' ontoCompare function like this: result <- ontoCompare(ProtNames, probeType = "Mus.musculus.GoMap.20070223") After a LONG time, it stops with the following: Error in as.vector(x, mode) : invalid argument 'mode' error Does anyone spot what I'm doing wrong? Thanks, Joh _______________________________________________ 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

Paquet, Agnes wrote: > OntoCompare will only work with the following probe types: Gene Ontology > ids, Affymetrix oligo Ids and Operon human and Mouse oligo ids. Other > types will not be recognized and you will get an error. Thanks so much for this clarification, but now I isolated all the GO terms for my data set and fed a list (14000 or so) of them to the function in 'result <- OntoCompare(list,probeType = "GO")' fashion and this results in a similar error: > GOs ... [14291] "GO:0003677" "GO:0004386" "GO:0005524" "GO:0016787" "GO:0001882" [14296] "GO:0003779" "GO:0005509" "GO:0005515" "GO:0042803" "GO:0051015" [14301] "GO:0003677" "GO:0003700" "GO:0005515" "GO:0008270" "GO:0043565" [14306] "GO:0046872" "GO:0000166" "GO:0003774" "GO:0003779" "GO:0005515" [14311] "GO:0005516" "GO:0005524" "GO:0005515" "GO:0046982" "GO:0003677" [14316] "GO:0004090" "GO:0016491" "GO:0000146" "GO:0000166" "GO:0003774" [14321] "GO:0003779" "GO:0005515" "GO:0005516" "GO:0005524" "GO:0016787" [14326] "GO:0016887" "GO:0030898" "GO:0042803" "GO:0043495" "GO:0043531" [14331] "GO:0051015" "GO:0003676" "GO:0008270" "GO:0046872" "GO:0005488" [14336] "GO:0005515" "GO:0008565" > result <- ontoCompare(GOs,probeType = "GO") [1] "Starting ontoCompare..." Error in as.vector(x, mode) : invalid argument 'mode' Am I still not getting this tool? Joh > > Best, > > Agnes > > ________________________________ > > From: > bioconductor-bounces at stat.math.ethz.ch on > behalf of Johannes Graumann Sent: Fri 2/23/2007 8:05 AM To: > bioconductor at stat.math.ethz.ch Subject: > [BioC] OntoCompare Error > > > > Hello, > > With the help of this list I succeeded in creating an annotation package > using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which > installs fine. > I then tried to run goTools' ontoCompare function like this: > > result <- ontoCompare(ProtNames, probeType = > "Mus.musculus.GoMap.20070223") > > After a LONG time, it stops with the following: > Error in as.vector(x, mode) : invalid argument 'mode' error > > Does anyone spot what I'm doing wrong? > > Thanks, Joh > > _______________________________________________ > 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

Hi Johannes, Did you feed a list of GO ids or a vector? of GO ids? I took some of your ids to try to reproduce the error but I didn't get any. Here is what I did: mygo=c("GO:0003677", "GO:0004386", "GO:0005524", "GO:0016787", "GO:0001882", "GO:0003779", "GO:0005509", "GO:0005515", "GO:0042803", "GO:0051015", "GO:0003677", "GO:0003700", "GO:0005515", "GO:0008270", "GO:0043565", "GO:0046872", "GO:0000166", "GO:0003774", "GO:0003779", "GO:0005515") ontoCompare(list(mygo),plot=T,probeType="GO") My R information is: > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: goTools GO annotate Biobase "1.6.0" "1.14.1" "1.12.0" "1.12.2" If you are feeding a vector of length 14000, ontoCompare is going to see your argument as a list of 14000 unique entities and that may be a reason for the error. If you are using the same type of input, could you please send me some of your GO ids in a .txt file, the command you are using and some information about which version of R, GO and goTools you are using so that I can reproduce the error and try to fix the problem? Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Johannes Graumann Sent: Mon 2/26/2007 4:16 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] OntoCompare Error Paquet, Agnes wrote: > OntoCompare will only work with the following probe types: Gene Ontology > ids, Affymetrix oligo Ids and Operon human and Mouse oligo ids. Other > types will not be recognized and you will get an error. Thanks so much for this clarification, but now I isolated all the GO terms for my data set and fed a list (14000 or so) of them to the function in 'result <- OntoCompare(list,probeType = "GO")' fashion and this results in a similar error: > GOs ... [14291] "GO:0003677" "GO:0004386" "GO:0005524" "GO:0016787" "GO:0001882" [14296] "GO:0003779" "GO:0005509" "GO:0005515" "GO:0042803" "GO:0051015" [14301] "GO:0003677" "GO:0003700" "GO:0005515" "GO:0008270" "GO:0043565" [14306] "GO:0046872" "GO:0000166" "GO:0003774" "GO:0003779" "GO:0005515" [14311] "GO:0005516" "GO:0005524" "GO:0005515" "GO:0046982" "GO:0003677" [14316] "GO:0004090" "GO:0016491" "GO:0000146" "GO:0000166" "GO:0003774" [14321] "GO:0003779" "GO:0005515" "GO:0005516" "GO:0005524" "GO:0016787" [14326] "GO:0016887" "GO:0030898" "GO:0042803" "GO:0043495" "GO:0043531" [14331] "GO:0051015" "GO:0003676" "GO:0008270" "GO:0046872" "GO:0005488" [14336] "GO:0005515" "GO:0008565" > result <- ontoCompare(GOs,probeType = "GO") [1] "Starting ontoCompare..." Error in as.vector(x, mode) : invalid argument 'mode' Am I still not getting this tool? Joh > > Best, > > Agnes > > ________________________________ > > From: > bioconductor-bounces at stat.math.ethz.ch on > behalf of Johannes Graumann Sent: Fri 2/23/2007 8:05 AM To: > bioconductor at stat.math.ethz.ch Subject: > [BioC] OntoCompare Error > > > > Hello, > > With the help of this list I succeeded in creating an annotation package > using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which > installs fine. > I then tried to run goTools' ontoCompare function like this: > > result <- ontoCompare(ProtNames, probeType = > "Mus.musculus.GoMap.20070223") > > After a LONG time, it stops with the following: > Error in as.vector(x, mode) : invalid argument 'mode' error > > Does anyone spot what I'm doing wrong? > > Thanks, Joh > > _______________________________________________ > 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 _______________________________________________ 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