GOstats with yeast2
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@sebastien-gerega-2229
Last seen 8.1 years ago
Hi, what is the best way to use GOstats (specifically a hyperG test on KEGG) with the yeast2.db annotation? I have looked around the mailing list archive and the fact that yeast2.db doesn't have a yeast2ENTREZID environment has been mentioned several times. However, I haven't managed to find any mention of how to get around this and use the annotation with GOstats. thanks, Sebastien
yeast2 GOstats yeast2 GOstats • 825 views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.4 years ago
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Hi Sebastien, There is no requirement that I am aware of for ENTREZIDs. All that is required is that you have some set of indentifiers (in this case yeast standard names seem most likely) that map to KEGG. And yeast2.db does seem to satisfy that requirement so I expect it would simply work. Perhaps you could show what you tried, what happened and your sessionInfo? best wishes Robert Sebastien Gerega wrote: > Hi, > what is the best way to use GOstats (specifically a hyperG test on KEGG) > with the yeast2.db annotation? I have looked around the mailing list > archive and the fact that yeast2.db doesn't have a yeast2ENTREZID > environment has been mentioned several times. However, I haven't managed > to find any mention of how to get around this and use the annotation > with GOstats. > thanks, > Sebastien > > _______________________________________________ > 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
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Hi Robert, here is the code I ran: params = new("GOHyperGParams", geneIds=sig, universeGeneIds = uni, annotation="yeast2.db", pvalueCutoff=0.05, testDirection="over", ontology = "BP") hgOver = hyperGTest(params) And I receive the following error: Error in get(mapName, envir = pkgEnv, inherits = FALSE) : variable "yeast2ENTREZID" was not found Error in mget(probes, ID2EntrezID(datPkg)) : error in evaluating the argument 'envir' in selecting a method for function 'mget' uni and sig contain affyIDs as follows: uni [1] "1769317_at" "1769320_at" "1769321_at" "1769322_s_at" "1769333_at" "1769336_at" "1769342_at" "1769350_at" "1769352_at" "1769366_at" "1769377_at" [12] "1769388_at" "1769406_at" "1769426_at" "1769428_at" "1769431_at" "1769443_at" "1769446_at" "1769450_at" "1769455_at" "1769472_at" "1769506_at" etc etc. sig [1] "1769579_at" "1769805_at" "1769955_at" "1770302_at" "1771153_at" "1771375_at" "1771705_at" "1772193_at" "1772642_at" "1772778_at" "1772785_at" "1773305_at" "1773699_at" [14] "1773961_at" "1774540_at" "1774742_at" "1775014_at" "1775340_at" "1775851_at" "1775890_at" "1775925_at" "1776156_at" "1776550_at" "1776829_at" "1777569_at" "1777690_at" [27] "1779266_at" "1779563_at" and finally: > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia. 1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2 altcdfenvs_2.2.0 [9] hypergraph_1.12.0 graph_1.18.0 Biostrings_2.8.0 makecdfenv_1.18.0 GDD_0.1-12 annaffy_1.12.0 KEGG.db_2.2.0 GO.db_2.2.0 [17] limma_2.14.0 affyPLM_1.16.0 gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 yeast2.db_2.2.0 [25] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 Biobase_2.0.0 yeast2cdf_2.2.0 loaded via a namespace (and not attached): [1] cluster_1.11.10 thanks for your help, Sebastien Robert Gentleman wrote: > Hi Sebastien, > There is no requirement that I am aware of for ENTREZIDs. All that > is required is that you have some set of indentifiers (in this case > yeast standard names seem most likely) that map to KEGG. And yeast2.db > does seem to satisfy that requirement so I expect it would simply work. > Perhaps you could show what you tried, what happened and your > sessionInfo? > > > best wishes > Robert > > > Sebastien Gerega wrote: >> Hi, >> what is the best way to use GOstats (specifically a hyperG test on >> KEGG) with the yeast2.db annotation? I have looked around the mailing >> list archive and the fact that yeast2.db doesn't have a >> yeast2ENTREZID environment has been mentioned several times. However, >> I haven't managed to find any mention of how to get around this and >> use the annotation with GOstats. >> thanks, >> Sebastien >> >> _______________________________________________ >> 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 Sebastien, I see, it seems that there are some issues in the GOstats/Category packages for dealing with this that need a fair bit of attention. I am sorry to say that this is likely to take a few weeks for me to sort out, but your report is most helpful. best wishes Robert Sebastien Gerega wrote: > Hi Robert, > here is the code I ran: > params = new("GOHyperGParams", geneIds=sig, universeGeneIds = uni, > annotation="yeast2.db", pvalueCutoff=0.05, testDirection="over", > ontology = "BP") > hgOver = hyperGTest(params) > > And I receive the following error: > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > variable "yeast2ENTREZID" was not found > Error in mget(probes, ID2EntrezID(datPkg)) : > error in evaluating the argument 'envir' in selecting a method for > function 'mget' > > uni and sig contain affyIDs as follows: > > uni > [1] "1769317_at" "1769320_at" "1769321_at" "1769322_s_at" > "1769333_at" "1769336_at" "1769342_at" "1769350_at" > "1769352_at" "1769366_at" "1769377_at" [12] "1769388_at" > "1769406_at" "1769426_at" "1769428_at" "1769431_at" > "1769443_at" "1769446_at" "1769450_at" "1769455_at" > "1769472_at" "1769506_at" > etc etc. > > sig > [1] "1769579_at" "1769805_at" "1769955_at" "1770302_at" "1771153_at" > "1771375_at" "1771705_at" "1772193_at" "1772642_at" "1772778_at" > "1772785_at" "1773305_at" "1773699_at" > [14] "1773961_at" "1774540_at" "1774742_at" "1775014_at" "1775340_at" > "1775851_at" "1775890_at" "1775925_at" "1776156_at" "1776550_at" > "1776829_at" "1777569_at" "1777690_at" > [27] "1779266_at" "1779563_at" > > and finally: > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi a.1252 > > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > other attached packages: > [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > xtable_1.5-2 altcdfenvs_2.2.0 [9] hypergraph_1.12.0 > graph_1.18.0 Biostrings_2.8.0 makecdfenv_1.18.0 > GDD_0.1-12 annaffy_1.12.0 KEGG.db_2.2.0 > GO.db_2.2.0 [17] limma_2.14.0 affyPLM_1.16.0 > gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 > preprocessCore_1.2.0 affyio_1.8.0 yeast2.db_2.2.0 [25] > AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 > Biobase_2.0.0 yeast2cdf_2.2.0 > loaded via a namespace (and not attached): > [1] cluster_1.11.10 > > thanks for your help, > Sebastien > > > Robert Gentleman wrote: >> Hi Sebastien, >> There is no requirement that I am aware of for ENTREZIDs. All that >> is required is that you have some set of indentifiers (in this case >> yeast standard names seem most likely) that map to KEGG. And yeast2.db >> does seem to satisfy that requirement so I expect it would simply work. >> Perhaps you could show what you tried, what happened and your >> sessionInfo? >> >> >> best wishes >> Robert >> >> >> Sebastien Gerega wrote: >>> Hi, >>> what is the best way to use GOstats (specifically a hyperG test on >>> KEGG) with the yeast2.db annotation? I have looked around the mailing >>> list archive and the fact that yeast2.db doesn't have a >>> yeast2ENTREZID environment has been mentioned several times. However, >>> I haven't managed to find any mention of how to get around this and >>> use the annotation with GOstats. >>> thanks, >>> Sebastien >>> >>> _______________________________________________ >>> 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
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Hi Robert, at least the error wasn't from me doing something wrong! can you think of any way around this problem? For example I could use GOstats with another yeast annotation DB but would then still have to map between affyID and some other type of identifier... thanks, Sebastien Robert Gentleman wrote: > Hi Sebastien, > I see, it seems that there are some issues in the GOstats/Category > packages for dealing with this that need a fair bit of attention. I > am sorry to say that this is likely to take a few weeks for me to sort > out, but your report is most helpful. > > best wishes > Robert > > > Sebastien Gerega wrote: >> Hi Robert, >> here is the code I ran: >> params = new("GOHyperGParams", geneIds=sig, universeGeneIds = uni, >> annotation="yeast2.db", pvalueCutoff=0.05, testDirection="over", >> ontology = "BP") >> hgOver = hyperGTest(params) >> >> And I receive the following error: >> Error in get(mapName, envir = pkgEnv, inherits = FALSE) : >> variable "yeast2ENTREZID" was not found >> Error in mget(probes, ID2EntrezID(datPkg)) : >> error in evaluating the argument 'envir' in selecting a method for >> function 'mget' >> >> uni and sig contain affyIDs as follows: >> >> uni >> [1] "1769317_at" "1769320_at" "1769321_at" "1769322_s_at" >> "1769333_at" "1769336_at" "1769342_at" "1769350_at" >> "1769352_at" "1769366_at" "1769377_at" [12] "1769388_at" >> "1769406_at" "1769426_at" "1769428_at" "1769431_at" >> "1769443_at" "1769446_at" "1769450_at" "1769455_at" >> "1769472_at" "1769506_at" >> etc etc. >> >> sig >> [1] "1769579_at" "1769805_at" "1769955_at" "1770302_at" "1771153_at" >> "1771375_at" "1771705_at" "1772193_at" "1772642_at" "1772778_at" >> "1772785_at" "1773305_at" "1773699_at" >> [14] "1773961_at" "1774540_at" "1774742_at" "1775014_at" "1775340_at" >> "1775851_at" "1775890_at" "1775925_at" "1776156_at" "1776550_at" >> "1776829_at" "1777569_at" "1777690_at" >> [27] "1779266_at" "1779563_at" >> >> and finally: >> > sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;L C_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austral ia.1252 >> >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets methods base other attached packages: >> [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 >> survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 >> xtable_1.5-2 altcdfenvs_2.2.0 [9] hypergraph_1.12.0 >> graph_1.18.0 Biostrings_2.8.0 makecdfenv_1.18.0 >> GDD_0.1-12 annaffy_1.12.0 KEGG.db_2.2.0 >> GO.db_2.2.0 [17] limma_2.14.0 affyPLM_1.16.0 >> gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 >> preprocessCore_1.2.0 affyio_1.8.0 yeast2.db_2.2.0 [25] >> AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 >> Biobase_2.0.0 yeast2cdf_2.2.0 loaded via a namespace (and >> not attached): >> [1] cluster_1.11.10 >> >> thanks for your help, >> Sebastien >> >> >> Robert Gentleman wrote: >>> Hi Sebastien, >>> There is no requirement that I am aware of for ENTREZIDs. All that >>> is required is that you have some set of indentifiers (in this case >>> yeast standard names seem most likely) that map to KEGG. And >>> yeast2.db does seem to satisfy that requirement so I expect it would >>> simply work. >>> Perhaps you could show what you tried, what happened and your >>> sessionInfo? >>> >>> >>> best wishes >>> Robert >>> >>> >>> Sebastien Gerega wrote: >>>> Hi, >>>> what is the best way to use GOstats (specifically a hyperG test on >>>> KEGG) with the yeast2.db annotation? I have looked around the >>>> mailing list archive and the fact that yeast2.db doesn't have a >>>> yeast2ENTREZID environment has been mentioned several times. >>>> However, I haven't managed to find any mention of how to get around >>>> this and use the annotation with GOstats. >>>> thanks, >>>> Sebastien >>>> >>>> _______________________________________________ >>>> 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 Sebastien, You could try to use the YEAST package (that seems to be the only one that is working, but it is going to be deprecated - so I will need to fix this in the next little while). From yeast2.db you can get ORFs (which is what will be used - mostly) in the YEAST package. So once you map both the sig and uni IDs to ORFs, you can use those two vectors and set the annotation to "YEAST". Robert Sebastien Gerega wrote: > Hi Robert, > at least the error wasn't from me doing something wrong! > can you think of any way around this problem? For example I could use > GOstats with another yeast annotation DB but would then still have to > map between affyID and some other type of identifier... > thanks, > Sebastien > > Robert Gentleman wrote: >> Hi Sebastien, >> I see, it seems that there are some issues in the GOstats/Category >> packages for dealing with this that need a fair bit of attention. I >> am sorry to say that this is likely to take a few weeks for me to sort >> out, but your report is most helpful. >> >> best wishes >> Robert >> >> >> Sebastien Gerega wrote: >>> Hi Robert, >>> here is the code I ran: >>> params = new("GOHyperGParams", geneIds=sig, universeGeneIds = uni, >>> annotation="yeast2.db", pvalueCutoff=0.05, testDirection="over", >>> ontology = "BP") >>> hgOver = hyperGTest(params) >>> >>> And I receive the following error: >>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) : >>> variable "yeast2ENTREZID" was not found >>> Error in mget(probes, ID2EntrezID(datPkg)) : >>> error in evaluating the argument 'envir' in selecting a method for >>> function 'mget' >>> >>> uni and sig contain affyIDs as follows: >>> >>> uni >>> [1] "1769317_at" "1769320_at" "1769321_at" "1769322_s_at" >>> "1769333_at" "1769336_at" "1769342_at" "1769350_at" >>> "1769352_at" "1769366_at" "1769377_at" [12] "1769388_at" >>> "1769406_at" "1769426_at" "1769428_at" "1769431_at" >>> "1769443_at" "1769446_at" "1769450_at" "1769455_at" >>> "1769472_at" "1769506_at" >>> etc etc. >>> >>> sig >>> [1] "1769579_at" "1769805_at" "1769955_at" "1770302_at" "1771153_at" >>> "1771375_at" "1771705_at" "1772193_at" "1772642_at" "1772778_at" >>> "1772785_at" "1773305_at" "1773699_at" >>> [14] "1773961_at" "1774540_at" "1774742_at" "1775014_at" "1775340_at" >>> "1775851_at" "1775890_at" "1775925_at" "1776156_at" "1776550_at" >>> "1776829_at" "1777569_at" "1777690_at" >>> [27] "1779266_at" "1779563_at" >>> >>> and finally: >>> > sessionInfo() >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252; LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austra lia.1252 >>> >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets methods base other attached packages: >>> [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 >>> survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 >>> xtable_1.5-2 altcdfenvs_2.2.0 [9] hypergraph_1.12.0 >>> graph_1.18.0 Biostrings_2.8.0 makecdfenv_1.18.0 >>> GDD_0.1-12 annaffy_1.12.0 KEGG.db_2.2.0 >>> GO.db_2.2.0 [17] limma_2.14.0 affyPLM_1.16.0 >>> gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 >>> preprocessCore_1.2.0 affyio_1.8.0 yeast2.db_2.2.0 [25] >>> AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 >>> Biobase_2.0.0 yeast2cdf_2.2.0 loaded via a namespace (and >>> not attached): >>> [1] cluster_1.11.10 >>> >>> thanks for your help, >>> Sebastien >>> >>> >>> Robert Gentleman wrote: >>>> Hi Sebastien, >>>> There is no requirement that I am aware of for ENTREZIDs. All that >>>> is required is that you have some set of indentifiers (in this case >>>> yeast standard names seem most likely) that map to KEGG. And >>>> yeast2.db does seem to satisfy that requirement so I expect it would >>>> simply work. >>>> Perhaps you could show what you tried, what happened and your >>>> sessionInfo? >>>> >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> Sebastien Gerega wrote: >>>>> Hi, >>>>> what is the best way to use GOstats (specifically a hyperG test on >>>>> KEGG) with the yeast2.db annotation? I have looked around the >>>>> mailing list archive and the fact that yeast2.db doesn't have a >>>>> yeast2ENTREZID environment has been mentioned several times. >>>>> However, I haven't managed to find any mention of how to get around >>>>> this and use the annotation with GOstats. >>>>> thanks, >>>>> Sebastien >>>>> >>>>> _______________________________________________ >>>>> 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
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