Well well,
I am ashamed to say that it is now working.

Apparently all I needed to do was to update the packages.

I installed the new version of GO.db and GOstats
and it is working now.

Also I am still getting this error when trying to find which genes are
attached to it.
> mget('GO:2000021',org.Mm.egGO)
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
  value for "GO:2000021" not found
> mget('GO:2000021',org.Mm.egGO2EG)
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "GO:2000021" not found

So I guess the earlier error message as nothing to do with the fact that
there are no genes from the mouse genome mapped to this GO category

When I checked in AmiGo to see if there are no genes from mouse under this
category, I found 83 genes.
Can anyone tell me than what's the meaning of this error?

Is there a way of manually update the GO data set, so that I can map these
genes?

Thanks
Assa

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines   grid      stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] GSEABase_1.12.1      org.Mm.eg.db_2.4.6   biomaRt_2.6.0
 [4] Heatplus_1.20.0      ggplot2_0.8.9        proto_0.3-9.1
 [7] reshape_0.8.4        plyr_1.4             gplots_2.8.0
[10] caTools_1.11         bitops_1.0-4.1       gdata_2.8.1
[13] gtools_2.6.2         siggenes_1.24.0      multtest_2.7.1
[16] Rgraphviz_1.29.0     xtable_1.5-6         annotate_1.28.1
[19] GO.db_2.4.5          GOstats_2.16.0       RSQLite_0.9-4
[22] DBI_0.2-5            graph_1.28.0         Category_2.16.0
[25] AnnotationDbi_1.12.0 Biobase_2.10.0

loaded via a namespace (and not attached):
[1] genefilter_1.32.0 MASS_7.3-11       RBGL_1.26.0       RCurl_1.5-0
[5] survival_2.36-5   tools_2.12.2      XML_3.2-0

On Thu, Apr 7, 2011 at 18:49, Robert M. Flight <rflight79@gmail.com> wrote:

> Hi Assa,
>
> As far as I am aware, if the GO term comes up in your list, then there
> should be genes annotated to it. I did a simple test to verify that
> the GO term does exist:
>
>  crud <- as.list(GOTERM)
> > crud$'GO:2000021'
> GOID: GO:2000021
> Term: regulation of ion homeostasis
> Ontology: BP
> Definition: Any process that modulates the frequency, rate or extent
> of ion homeostasis.
> Synonym: regulation of electrolyte homeostasis
> Synonym: regulation of negative regulation of crystal biosynthesis
> Synonym: regulation of negative regulation of crystal formation
>
> So far so good. Now lets look to see what genes are annotated to it:
>
> > library(org.Mm.eg.db)
> > mget('GO:2000021',org.Mm.egGO)
> Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
>  value for "GO:2000021" not found
>
> > mget('GO:2000021',org.Mm.egGO2EG)
> Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
>  value for "GO:2000021" not found
> > mget('GO:2000021',org.Mm.egGO2ALLEGS)
> $`GO:2000021`
>     ISO      ISO      ISO      ISO      IGI      IGI      IMP
> IGI      ISO      ISO      IMP      ISO      ISO      IDA
>  "11517"  "11684"  "11998"  "12000"  "12018"  "12028"  "12028"
> "12043"  "12061"  "12257"  "12291"  "12349"  "12372"  "12389"
>     ISO      ISO      ISO      ISO      ISO      IMP      ISO
> ISO      IDA      IMP      IMP      IGI      IGI      ISO
>  "12424"  "12558"  "13167"  "13489"  "13617"  "13666"  "14062"
> "14126"  "14225"  "14225"  "14226"  "14629"  "14630"  "14652"
>     ISO      IDA      IDA      ISO      IDA      ISO       IC
> ISO      IMP      IMP      IDA      IMP      ISO      ISO
>  "15171"  "15978"  "16818"  "16867"  "16963"  "17096"  "17131"
> "18429"  "18439"  "18764"  "19264"  "20190"  "21333"  "21336"
>     ISO      ISO      IMP      ISO      ISO      TAS      IDA
> ISO      ISO      ISO      ISO      ISO      ISO      ISO
>  "21803"  "21808"  "21819"  "21838"  "22041"  "22784"  "23832"
> "24111"  "26361"  "50849"  "54140"  "76055"  "76757" "108837"
>     ISO      IMP      ISO      ISO      IMP      ISO
> "217369" "225908" "233081" "238276" "259277" "317757"
>
> BTW, this was all using GO.db_2.4.5
>
> From this information, there are no genes that are directly annotated
> to your GO term, only indirect annotations. I know this doesn't help
> your current situation, but it points towards the problem at least. I
> thought, however, when the summary was being prepared that it used the
> GO2ALLEGS mapping, and not the direct one. Perhaps someone more
> knowledgeable can figure out where in the code the error is likely to
> be?
>
> -Robert
>
> Robert M. Flight, Ph.D.
> University of Louisville Bioinformatics Laboratory
> University of Louisville
> Louisville, KY
>
> PH 502-852-1809 (HSC)
> PH 502-852-0467 (Belknap)
> EM robert.flight@louisville.edu
> EM rflight79@gmail.com
>
> Williams and Holland's Law:
>        If enough data is collected, anything may be proven by
> statistical methods.
>
>
>
> On Thu, Apr 7, 2011 at 11:22, Assa Yeroslaviz <frymor@gmail.com> wrote:
> > Hi,
> >
> > I am trying to run a HyerGTest with GOstats on a mouse genome entrez IDs.
> >
> > The Ids I have imported from biomart:
> > entrez_data_1 <- getBM(attributes=c("mgi_id","entrezgene"), filters=
> > "mgi_id", values = as.character(data_1$MGI),mart = mart)
> > head(entrez_data_1)
> > entrezID_Universe <-getBM(mart = mart, attributes = c("mgi_id",
> > "entrezgene"), filters ="mgi_id", values =as.character(MaxQuant18$MGI))
> > entrezID_Universe
> > params <- new("GOHyperGParams", geneIds =
> as.character(entrez_data_1[,2]),
> > universeGeneIds = as.character(entrezID_Universe[,2]), annotation =
> > "org.Mm.eg.db", ontology = "BP", pvalueCutoff = 0.05, conditional =
> FALSE,
> > testDirection = "over")
> > I Than tried to run the HyperGTest command with success
> > MmOverBP <- hyperGTest(paramsBP)
> > MmOverBP
> > Gene to GO BP  test for over-representation
> > 3146 GO BP ids tested (118 have p < 0.05)
> > Selected gene set size: 1006
> >    Gene universe size: 2935
> >    Annotation package: org.Mm.eg
> > but than:
> > summary(MmOverBP)
> >> summary(MmOverBP)
> > Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
> >  value for "GO:2000021" not found
> >
> > As far as I know, I have the latest version of both packages. I looked in
> > AmiGO whether this GO Id exists: it does.
> > AccessionGO:2000021OntologyBiological ProcessSynonymsrelated: regulation
> of
> > electrolyte homeostasis related: regulation of negative regulation of
> > crystal biosynthesisrelated: regulation of negative regulation of crystal
> > formation Is there a way of putting/annotating this specific item
> manually,
> > so that I can see it?
> > If not-
> > Is there a way of extracting this GO ID from the list of GO categories,
> so
> > that I can see the results?
> >
> > Thanks a lot
> > Assa
> >
> >
> >> sessionInfo()
> > R version 2.12.2 (2011-02-25)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] splines   grid      stats     graphics  grDevices utils     datasets
> > [8] methods   base
> >
> > other attached packages:
> >  [1] GO.db_2.4.1          org.Mm.eg.db_2.4.6   biomaRt_2.6.0
> >  [4] Heatplus_1.20.0      gplots_2.8.0         caTools_1.11
> >  [7] bitops_1.0-4.1       gdata_2.8.1          gtools_2.6.2
> > [10] siggenes_1.24.0      multtest_2.7.1       Rgraphviz_1.29.0
> > [13] xtable_1.5-6         annotate_1.28.1      GOstats_2.16.0
> > [16] RSQLite_0.9-4        DBI_0.2-5            graph_1.28.0
> > [19] Category_2.16.0      AnnotationDbi_1.12.0 Biobase_2.10.0
> >
> > loaded via a namespace (and not attached):
> > [1] genefilter_1.32.0 GSEABase_1.12.1   MASS_7.3-11       RBGL_1.26.0
> > [5] RCurl_1.5-0       survival_2.36-5   tcltk_2.12.2      tools_2.12.2
> > [9] XML_3.2-0
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > 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
> >
>

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