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

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 >