[BioC] how to remove affymetrix control probe sets from a an expression set

[Juliet Hannah]

The control names start with AFFX, so you can also:

library(affy)
mycels <-ReadAffy()
myRMA <- rma(mycels)
e = exprs(myRMA)
controls <- grep("AFFX",rownames(e))
e <- e[-controls,]

On Sat, Feb 18, 2012 at 5:05 AM, Yuan Hao <yuan.x.hao at gmail.com> wrote:
> You can check out the genefilter package
>
> http://www.bioconductor.org/packages/release/bioc/html/genefilter.html
>
> Cheers,
> Yuan
>
>
> On 18 Feb 2012, at 09:33, Salwa Eid wrote:
>
>>
>>
>>
>>
>> Dear all,   I read cel files from ncbi website using the readaffy().  Then
>> i performed the expresso function to normalize using quantile normalization
>> and retrieve rma expressions.  Next I want to remove the affymetrix control
>> probe sets from these expressions.  Any help? Thanks,salwa
>>
>>        [[alternative HTML version deleted]]
>>
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