[BioC] GEOquery, Limma Annotations

[Ovokeraye Achinike-Oduaran]

Nevermind. My bad. Sorted.

-Avoks

On Tue, Oct 4, 2011 at 8:18 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> 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
>