Hi Martin,
Session Info:
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] affy_1.26.1          GOstats_2.14.0       graph_1.28.0
Category_2.14.0      mouse4302.db_2.4.1   org.Mm.eg.db_2.4.1
RSQLite_0.9-2
 [8] DBI_0.2-5            AnnotationDbi_1.10.2 Biobase_2.8.0

loaded via a namespace (and not attached):
 [1] affyio_1.16.0         annotate_1.26.1       genefilter_1.30.0
GO.db_2.4.1           GSEABase_1.10.0       preprocessCore_1.10.0
 [7] RBGL_1.26.0           splines_2.11.1        survival_2.35-8
tools_2.11.1          XML_3.1-1             xtable_1.5-6


Commands used to create the mapping:
Library(mouse4302.db)
id <- rownames(allMtb.rma.data.frame)
map <- mouse4302ENTREZID
probe_entrezid <- unlist(mget(id, map))
p <- as.data.frame(probe_entrezid)
p now has the probeID_entrezID mappings

Thanks,
Anjan


On Tue, Nov 2, 2010 at 2:16 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 11/02/2010 11:14 AM, ANJAN PURKAYASTHA wrote:
> > Hi,
> > I have run into the following problem. I created a probeID-EntrezID
> mapping
> > for the Affy mouse array from the cognate annotation file Mouse4302.db.
> > Unfortunately about 10000 genes do not have corresponding EntrezID.
> > Many of these are genes with known functions. If I cannot map a EntrezID
> to
> > these then I cannot retrieve GO annotations and consequently I cannot do
> a
> > Gene Set Enrichment analysis using GOstats.
> > Does anyone have an update annotation file?
>
> Hi Anjan
>
> What is your sessionInfo() (else how could we know what an 'updated'
> annotation file is?) and how did you preform the mapping (short,
> hopefully reproducible, code)?
>
> Martin
>
> > Many thanks in advance,
> > Anjan
> >
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



-- 
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================

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