Use exprs on the output from RMA (or another method you like)
library("affy")
myData <-ReadAffy()
myRMA <- rma(myData)
e = exprs(myRMA)
Also, check out the Bioconductor mailing list where
Bioconductor-related topics are discussed.
On Fri, Apr 1, 2011 at 9:54 AM, Landes, Ezekiel
<ezekiel_lan...@hms.harvard.edu> wrote:
> I have an Affybatch object called "batch" :
>
>>
>> batch
> AffyBatch object
> size of arrays=1050x1050 features (196 kb)
> cdf=HuGene-1_0-st-v1 (32321 affyids)
> number of samples=384
> number of genes=32321
> annotation=hugene10stv1
> notes=
>>
>>
>
> Is there a way of converting a portion of this data into a matrix? More
> specifically, a matrix where the 384 samples are columns and the 32321 genes
> are rows? The "exprs" function returns a matrix that has 384 columns but for
> some reason there are 1050^2 rows.
>
> Thanks!
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>
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