ontoCompare

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Oana VIGY ▴ 80

@oana-vigy-3597

Last seen 10.3 years ago

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]<guest@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. > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives:http://news.gmane.org/gmane.science.biology.info rmatics.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 <http: www.fpp.cnrs.fr=""> -- Passerelle antivirus IGF [[alternative HTML version deleted]]

GO GO • 1.2k views

ADD COMMENT • link updated 12.4 years ago by Brad Davis ▴ 20 • written 12.4 years ago by Oana VIGY ▴ 80

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Brad Davis ▴ 20

@brad-davis-5385

Last seen 9.9 years ago

Canada

Hi Oana, I suspect the problem is actually with GO.db rather than goTools. The problems I ran in to involved GO terms that were either deprecated or where alternate IDs for the main GO ID. My workaround for this was to take my list of GO ids and compare it to the list of deprecated GO terms , removing any that match- then as the program would run, I'd keep a manual list of GO ids that didn't work because of the alternate id problem, and I had a little script I wrote to pre-emptively find and change those to the main GO ids which did work. Brad On Wed, Aug 8, 2012 at 4:41 AM, Oana VIGY <oana.vigy@igf.cnrs.fr> wrote: > 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] <guest@bioconductor.org> <guest@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. > > _______________________________________________ > Bioconductor mailing listBioconductor@r-project.orghttps://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]]

ADD COMMENT • link 12.4 years ago Brad Davis ▴ 20

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Hi Brad, thanks for your explanations and advices. It's meaningful. Best regards, Oana Le 08/08/2012 20:00, Brad Davis a écrit : > Hi Oana, > > I suspect the problem is actually with GO.db rather than goTools. The > problems I ran in to involved GO terms that were either deprecated or > where alternate IDs for the main GO ID. My workaround for this was to > take my list of GO ids and compare it to the list of deprecated GO > terms , removing any that match- then as the program would run, I'd > keep a manual list of GO ids that didn't work because of the alternate > id problem, and I had a little script I wrote to pre-emptively find > and change those to the main GO ids which did work. > > Brad > > > On Wed, Aug 8, 2012 at 4:41 AM, Oana VIGY <oana.vigy@igf.cnrs.fr> <mailto:oana.vigy@igf.cnrs.fr>> wrote: > > 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]<guest@bioconductor.org> <mailto:guest@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 atbioconductor.org <http: bioconductor.org="">. >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto: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 > <mailto: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 <http: www.fpp.cnrs.fr=""> > > > > > -- > Passerelle antivirus IGF > > > > -- > Passerelle antivirus IGF -- *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 <http: www.fpp.cnrs.fr=""> -- Passerelle antivirus IGF [[alternative HTML version deleted]]

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