[BioC] GOstats problem with output

[Marc Carlson]

Hi Assa,

The error that you reported suggests that the GO ID you have mapped to 
an entrez gene ID inside of your org.Mm.eg.db (which is where that 
GO2ALL mapping is from) is not present in your GO.db package so I think 
we should start by looking to see if your GO.db package is up to date.

Looking at your sessionInfo() I can see that you have an old stale 
version of GO.db  (2.4.1).  You should be using GO.db version 2.4.5 if 
you want to use org.Mm.eg.db version 2.4.6.  The annotations that are 
released for each version of Bioconductor are meant to be used as a 
matched set.  You can avoid having to worry about all of this using 
biocLite() to install all of the packages that you plan to use.  
biocLite() should always install the appropriate version of a given 
Bioconductor package for whichever version of R you happen to be running.

You can read about biocLite() here on our website where we explain how 
to install and update packages for Bioconductor:

http://www.bioconductor.org/install/



   Marc



On 04/07/2011 08:22 AM, Assa Yeroslaviz 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 at 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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>
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