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

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