Question: Problem with hyperGTest using ath1121501.db
0
gravatar for Ulrike Goebel
10.4 years ago by
Ulrike Goebel110
Ulrike Goebel110 wrote:
Dear list, I seem to have a problem with an obsolote GO id in ath1121501.db. >paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ; >hgCondOver <- hyperGTest(paramsCondOver) ; > summary(hgCondOver) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "GO:0006118" not found The GO database release 2009-05-10 says "This term was made obsolete because it describes a molecular function." Having realized this, I removed all gene ids from both H3K27me3_BP and uBP that had this term as sole annotation. But the error persists. (This is the only case where I had a problem with ath1121501.db's new capability of using AGIs -- normally it works fine !) H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) identifiers. The lists are too long to post, but I could send them if needed. > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.2.11 ath1121501.db_2.2.11 GOstats_2.10.0 [4] RSQLite_0.7-1 DBI_0.2-4 graph_1.22.2 [7] Category_2.10.0 AnnotationDbi_1.6.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 genefilter_1.24.0 GSEABase_1.6.0 RBGL_1.20.0 [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.3-0 [9] xtable_1.5-5 -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121
annotation go ath1121501 • 680 views
ADD COMMENTlink modified 10.4 years ago • written 10.4 years ago by Ulrike Goebel110
Answer: Problem with hyperGTest using ath1121501.db
0
gravatar for Ulrike Goebel
10.4 years ago by
Ulrike Goebel110
Ulrike Goebel110 wrote:
Thanks a lot, Marc -- it works now ! Ulrike mcarlson at fhcrc.org schrieb: > Hi Ulrike, > > Thanks for pointing this out. I have just updated this package for > you. Please try out the ath1121501.db_2.2.12.tar.gz version and let > me know if you have any other problems with it. > > > Marc > > > > > Quoting Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de="">: > >> Dear list, >> >> I seem to have a problem with an obsolote GO id in ath1121501.db. >> >>> paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, >> universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", >> pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ; >>> hgCondOver <- hyperGTest(paramsCondOver) ; >>> summary(hgCondOver) >> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >> value for "GO:0006118" not found The GO database release >> 2009-05-10 says "This term was made obsolete because it describes a >> molecular function." Having realized this, I removed all gene ids from >> both H3K27me3_BP and uBP that had this term as sole annotation. But >> the error persists. (This is the only case where I had a problem with >> ath1121501.db's new capability of using AGIs -- normally it works fine >> !) >> >> H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) >> identifiers. The lists are too long to post, but I could send them if >> needed. >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GO.db_2.2.11 ath1121501.db_2.2.11 GOstats_2.10.0 >> [4] RSQLite_0.7-1 DBI_0.2-4 graph_1.22.2 >> [7] Category_2.10.0 AnnotationDbi_1.6.0 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.22.0 genefilter_1.24.0 GSEABase_1.6.0 RBGL_1.20.0 >> [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.3-0 >> [9] xtable_1.5-5 >> >> >> >> >> >> -- >> Dr. Ulrike Goebel >> Bioinformatics Support >> Max-Planck Institute for Plant Breeding Research >> Carl-von-Linne Weg 10 >> 50829 Cologne >> Germany >> +49(0) 221 5062 121 >> >> _______________________________________________ >> 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 > > > -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121
ADD COMMENTlink written 10.4 years ago by Ulrike Goebel110
Hi Marc, well, now I get > summary(hgCondUnder) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "GO:0044085" not found with the same lists and test direction "under". Strange, because this GO term does exist ! Regards, Ulrike Ulrike Goebel schrieb: > Thanks a lot, Marc -- it works now ! > > Ulrike > > mcarlson at fhcrc.org schrieb: >> Hi Ulrike, >> >> Thanks for pointing this out. I have just updated this package for >> you. Please try out the ath1121501.db_2.2.12.tar.gz version and let >> me know if you have any other problems with it. >> >> >> Marc >> >> >> >> >> Quoting Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de="">: >> >>> Dear list, >>> >>> I seem to have a problem with an obsolote GO id in ath1121501.db. >>> >>>> paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, >>> universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", >>> pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ; >>>> hgCondOver <- hyperGTest(paramsCondOver) ; >>>> summary(hgCondOver) >>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >>> value for "GO:0006118" not found The GO database release >>> 2009-05-10 says "This term was made obsolete because it describes a >>> molecular function." Having realized this, I removed all gene ids from >>> both H3K27me3_BP and uBP that had this term as sole annotation. But >>> the error persists. (This is the only case where I had a problem with >>> ath1121501.db's new capability of using AGIs -- normally it works fine >>> !) >>> >>> H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) >>> identifiers. The lists are too long to post, but I could send them if >>> needed. >>> >>>> sessionInfo() >>> R version 2.9.0 (2009-04-17) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID ENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] GO.db_2.2.11 ath1121501.db_2.2.11 GOstats_2.10.0 >>> [4] RSQLite_0.7-1 DBI_0.2-4 graph_1.22.2 >>> [7] Category_2.10.0 AnnotationDbi_1.6.0 Biobase_2.4.1 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.22.0 genefilter_1.24.0 GSEABase_1.6.0 RBGL_1.20.0 >>> [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.3-0 >>> [9] xtable_1.5-5 >>> >>> >>> >>> >>> >>> -- >>> Dr. Ulrike Goebel >>> Bioinformatics Support >>> Max-Planck Institute for Plant Breeding Research >>> Carl-von-Linne Weg 10 >>> 50829 Cologne >>> Germany >>> +49(0) 221 5062 121 >>> >>> _______________________________________________ >>> 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 >> >> >> > > -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121
ADD REPLYlink written 10.4 years ago by Ulrike Goebel110
Hi Ulrike, I have also tracked down this problem (which was different) and eliminated it as well. Thank you for letting me know about it! You should move on to the 2.2.13 version of the ath1121501.db package at this time. Please let me know if you have any other troubles after upgrading. Marc Ulrike Goebel wrote: > Hi Marc, > > well, now I get > > summary(hgCondUnder) > Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : > value for "GO:0044085" not found > > with the same lists and test direction "under". Strange, because this > GO term does exist ! > > Regards, Ulrike > > Ulrike Goebel schrieb: >> Thanks a lot, Marc -- it works now ! >> >> Ulrike >> >> mcarlson at fhcrc.org schrieb: >>> Hi Ulrike, >>> >>> Thanks for pointing this out. I have just updated this package for >>> you. Please try out the ath1121501.db_2.2.12.tar.gz version and let >>> me know if you have any other problems with it. >>> >>> >>> Marc >>> >>> >>> >>> >>> Quoting Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de="">: >>> >>>> Dear list, >>>> >>>> I seem to have a problem with an obsolote GO id in ath1121501.db. >>>> >>>>> paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, >>>> universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", >>>> pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ; >>>>> hgCondOver <- hyperGTest(paramsCondOver) ; >>>>> summary(hgCondOver) >>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >>>> value for "GO:0006118" not found The GO database release >>>> 2009-05-10 says "This term was made obsolete because it describes a >>>> molecular function." Having realized this, I removed all gene ids from >>>> both H3K27me3_BP and uBP that had this term as sole annotation. But >>>> the error persists. (This is the only case where I had a problem with >>>> ath1121501.db's new capability of using AGIs -- normally it works fine >>>> !) >>>> >>>> H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) >>>> identifiers. The lists are too long to post, but I could send them if >>>> needed. >>>> >>>>> sessionInfo() >>>> R version 2.9.0 (2009-04-17) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GO.db_2.2.11 ath1121501.db_2.2.11 GOstats_2.10.0 >>>> [4] RSQLite_0.7-1 DBI_0.2-4 graph_1.22.2 >>>> [7] Category_2.10.0 AnnotationDbi_1.6.0 Biobase_2.4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.22.0 genefilter_1.24.0 GSEABase_1.6.0 RBGL_1.20.0 >>>> [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.3-0 >>>> [9] xtable_1.5-5 >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Ulrike Goebel >>>> Bioinformatics Support >>>> Max-Planck Institute for Plant Breeding Research >>>> Carl-von-Linne Weg 10 >>>> 50829 Cologne >>>> Germany >>>> +49(0) 221 5062 121 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> > >
ADD REPLYlink written 10.4 years ago by Marc Carlson7.2k
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