Dear Agnes, I encountered a similar issue last summer (see related messages on the list - August 2011) and exchanged few emails directly with Jean about that (+copy to you). I'm using the "goTools" package in a script which is working fine for few years with the given system : R 2.5.1 and BioConductor 2.0.8 (goTools 1.8) and I try several times to upgrade R & Co. but I faced then the kind of problem which was reported by Brad and time-consuming problems. It's quite difficult to maintain an old system and perhaps it is a non-sense to continue performing analysis with the old package. Please let us know how it goes. Best regards, Oana Le 12/07/2012 22:01, Agnes Paquet a écrit : > Hi Brad, > > I will take a look and see if there is an easy fix. Sorry for the trouble you are having using the package. > > Agnes > > On Jul 12, 2012, at 12:29 PM, Brad Davis [guest] wrote: > >> Hello everyone, >> >> I am having some difficulty with ontoCompare when providing it with a list of GO terms. Here is an example of the output that I get when the function fails: >> >> >>> ontoTest <- ontoCompare(list(gotermslist), probeType="GO", goType="BP", plot=TRUE) >> Starting ontoCompare... >> Error in goidvect[test] : invalid subscript type 'list' >> >> Enter a frame number, or 0 to exit >> >> 1: ontoCompare(list(gotermslist), probeType = "GO", goType = "BP", plot = TRUE) >> 2: lapply(tmp, parentsVectWraper, endnode) >> 3: FUN(X[[2554]], ...) >> >>> gotermslist[2554] >> [1] "GO:0051605" >> >> Using Amigo to look up this GO term shows this GO ID is an alternate ID to GO:0016485, but using the Synonym function from GO.db on GO:0051605 doesn't provide any useful information. >> >> >>> Synonym("GO:0051605") >> $ >> NULL >> >> Conversely, running Synonym on GO:0016485 identifies GO:0051605 as a valid alternate id >> >> >>> Synonym("GO:0016485") >> $`GO:0016485` >> [1] "peptidolysis during protein maturation" >> [2] "protein maturation by peptide bond cleavage" >> [3] "protein maturation by peptide bond hydrolysis" >> [4] "protein maturation by proteolysis" >> [5] "GO:0051605" >> >> I run into the same problem with GO:0006345, which is an alternate ID for GO:0031936 (which doesn't cause a problem for ontoCompare). >> >> It seems like this represents some sort of mapping problem with GO.db, but I don't know how to address it myself. Any suggestions? >> >> In other cases, ontoCompare fails when there doesn't seem to be any problem with the GO id, at least so far as I can tell, e.g. GO:0055086. Amigo doesn't show any alternate ids nor does it indicate that the term is obsolete, so I don't understand why it's not working- but it is very frustrating. >> >> I would appreciate any suggestions. >> >> >> >> >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 >> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C >> [5] LC_TIME=English_Canada.1252 >> >> attached base packages: >> [1] compiler grid stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] Vennerable_2.2 xtable_1.7-0 reshape_0.8.4 plyr_1.7.1 >> [5] RColorBrewer_1.0-5 lattice_0.20-6 RBGL_1.30.1 graph_1.32.0 >> [9] manipulate_0.96.316 annotate_1.32.3 goTools_1.28.0 GO.db_2.6.1 >> [13] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.19 Biobase_2.14.0 >> [17] nlme_3.1-104 car_2.0-12 nnet_7.3-4 gplots_2.11.0 >> [21] MASS_7.3-19 KernSmooth_2.23-8 caTools_1.13 bitops_1.0-4.1 >> [25] gdata_2.11.0 gtools_2.7.0 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.12.6 tools_2.15.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. > _______________________________________________ > 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 > -- *Oana VIGY* *! Changement d'adresse email : oana.vigy@fpp.cnrs.fr !* Plate-forme de Protéomique Fonctionnelle (FPP) c/o IGF, UMR 5203 CNRS - INSERM U661 - UM1 - UM2 141 rue de la Cardonille 34 094 Montpellier Cedex 5, France ------------------------------------------------------------------------ Tel: +33 (0)4 34 35 92 39 www.fpp.cnrs.fr -- Passerelle antivirus IGF [[alternative HTML version deleted]]