Hi All,

I am having some trouble to do the annotation of the normalized genes for a set of Affymetrix file (cdf = HG-U133_Plus_2) using UniGene ID and then, creating the output table.

I was mainly referring to the book, "Bioinformatics & Computational Biology Solutions Using R and Bioinformatics" but at one stage, I was unsure as to how to proceed.

Any suggestion would be appreciated. Also, wonder if there is any other (quicker!) way of doing it !

Thank you !

Cheers,

Chintanu



> myRMA <- justRMA()
> probeids4log2 <- featureNames (myRMA)
> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db")
> anncols <- aaf.handler ()[c(1,2,7,9)]
> anntable4log2 <- aafTableAnn (probeids4log2, "hgu133plus2.db", anncols)
> exprtable4log2 <- aafTableInt (myRMA, probeids=probeids4log2)
> table4log2 <- merge (anntable4log2, exprtable4log2)
> UniGeneID4log2 <-  table4log2$UniGene
#  genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2)
> sessionInfo ()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
 [1] hgu133a2.db_2.2.11    hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0     siggenes_1.18.0       annaffy_1.16.0        KEGG.db_2.2.11
 [7] GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4             AnnotationDbi_1.6.0   multtest_2.0.0        affy_1.22.0
[13] Biobase_2.4.1
loaded via a namespace (and not attached):
[1] affyio_1.12.0        MASS_7.2-46          preprocessCore_1.6.0 survival_2.35-4      tools_2.9.0

	[[alternative HTML version deleted]]

