Hi,

I think you can first convert AffyBatch obejct into ExpressionSet data type
(by using preprocessing algorithms like rma, plier, gcrma etc) and than by
using method 'exprs' you should get full matrix with probe names....

>>>sample code

library(affy)
#Import cel files into R
data<-ReadAffy()
#preprocess AffyBatch object 'data' with RMA
data2<-rma(data)
#extracting matrix
data3<-exprs(data2)
#converting matrix to data frame
data4<-as.data.frame(data3)
names(data4)[1]<-"ProbesetID"
#exporting data matrix to external tab-delimited file for downstream
analysis
write.table(data4,"Data.txt",sep="\t")
<<<<<<


Best Regards,

Saurabh

On Wed, May 18, 2011 at 1:16 PM, Assa Yeroslaviz <frymor@gmail.com> wrote:

> Hi,
>
> I'm trying to extract a matrix of intensity values from an AffyBatch
> object.
>
> I know I can have them using
> > Intensity(AffyBatch)
> or
> >exprs(AffyBatch)
>
> but I would like to have a full matrix with the probe names.
> Unfortunately I can't find a way of doing it.
>
> There are several way of extracting the names of the probes, but not in the
> same order or magnitude compared to the intensity array.
>
> > length(geneNames(rawData))[1] 18952> length(probeNames(rawData))[1]
> 265358> dim(intensity(rawData))[1] 535824     12> dim(exprs(rawData))[1]
> 535824     12
>
> Does anyone has an idea of how to extract these Values into a matrix. I
> have
> the original CEL files.
>
> Even a way outside of R will be welcome.
>
> Thanks
>
> Assa
>
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