[BioC] Affy output

[James W. MacDonald]

Hi Chintanu,

Sarmah, Chintanu Kumar wrote:
> 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 !

I'm not sure what trouble you are having - I don't see any error 
messages below, so I assume the code runs?

Anyway, there are easier ways to do this. One such way is using 
probes2table() in affycoretools.

probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", 
aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data")

Best,

Jim


> 
> 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]]
> 
> _______________________________________________ Bioconductor mailing
> list Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
> archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826