[BioC] GEOquery, Limma Annotations
Ovokeraye Achinike-Oduaran
ovokeraye at gmail.com
Tue Oct 4 08:18:19 CEST 2011
Hi all,
Can I please get some help with including a code to the script below
to get the actual annotation for the resulting gene list not just the
platform clone_id?
It will be greatly appreciated. Thanks.
Regards,
Avoks
gds157dat = getGEO('GDS157',destdir=".")
gds157eset = GDS2eSet(gds157dat, do.log2=TRUE)
m = pData(gds157eset)$metabolism
design_gds157 = createDesignMatrix(gds157eset)
design_gds157 = model.matrix(~m)
fit = lmFit(gds157eset, design_gds157)
fit2 = eBayes(fit)
results = topTable(fit2, adjust ="BH", number = nrow(gdseset))
excel = write.table(results, file = "C:/Documents and Settings/xxx)
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_xxx. LC_CTYPE=English_xxx
[3] LC_MONETARY=English_xxx LC_NUMERIC=C
[5] LC_TIME=English_xxx
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] puma_2.4.0 mclust_3.4.10 affy_1.30.0 limma_3.8.3
[5] GEOquery_2.19.4 Biobase_2.12.2
loaded via a namespace (and not attached):
[1] affyio_1.20.0 preprocessCore_1.14.0 RCurl_1.6-10.1
[4] tools_2.13.1 XML_3.4-2.2
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