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") $<na> 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 Amigo doesn't show any alternate ids nor does it indicate that the term is obsolete, so I don't understand why it's not working- but it is very frustrating.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.

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] <guest at="" bioconductor.org=""> 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") > $<na> > 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.