Remove Probes from Raw .CEL Files - AFFY HG-U133-Plus2.0

Question

[Alex Gibbs]

Hi all,

I have multiple Accessions(13) that I'm combining to analyse data(~2000 samples). All of the Accessions have the same platform (GPL570).

After investigating all the Accessions, I noticed that one of them (E-MTAB-3444) has around 300 extra probes added to the platform. This means that I cannot analyse it the same time as the other samples..

The way I analyse my samples is to download each samples .CEL file, import them all into R, and normalise using RMA.

My question is, How can I go about removing these extra probes from the .CEL files, so that I can run the analysis all at once?

Thanks in advance,

Alex.