[BioC] Removing bad probesets

[Hairong Wei]

I have to analyse some data from MG_U74 chips that contain 2613 bad
probesets (antisense DNA strand)  resulted from a mistake of Affymetrix.
I need to remove these bad probeset from CEL file before I regenerate data
(from CEL files ) because some algorithms e.g. RMA, may use these bad
probesets to do normalization.    I called Affymetrix but was told that
their mask files can remove bad probesets only after data is regerated from
CEL files.    
 
For anybody who has experience in such a thing or has knowledge on how to
resolve this issue, please give some suggestions.     
 
Hairong


 

 

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