[BioC] GEOquery, Limma Annotations

[Ovokeraye Achinike-Oduaran]

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