[BioC] Removing bad probesets

Ben Bolstad bolstad at stat.berkeley.edu
Tue Mar 15 00:00:26 CET 2005

At least as far as rma() goes, you can use the "subset" argument to
specify a list of probesets to restrict to for all calculations (ie the
other probesets and their probe intensities are entirely ignored).


On Mon, 2005-03-14 at 15:52 -0600, Hairong Wei wrote:
> 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
> 	[[alternative HTML version deleted]]
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