[BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray

Virginia Garcia virginia.garcia at ifi.csic.es
Tue Jun 21 12:46:16 CEST 2011

Dear list,

I am quite new to R as well as to microarray analysis.
I am dealing with some gene expression analysis performed on Affymetrix Human 
Gene 1.0ST microarray. 

So far, I have learnt how to filtrate data using genefilter using nsFilter 

Now, I would like to know how to filter out from the expressionset object all 
the control probesets (~4000) that Affymetrix includes in the microarray (for 
quality assay, normalization, background correction, etc.). However, none of 
the aforementioned functions worked for me. 

How can I recognize those probesets and remove them? I would like to filter 
them out before statistical analysis with limma package.

Thank you very much in advance for your help.


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