[BioC] Affymetrix Chips with Missing Spike-Ins

[Rafael A. Irizarry]

the easiste thing to do is change the cdf environment to not include those 
probesets. the "dealing_with_cdfenvs" vignette has some useful 
information. 




On Fri, 18 Jul 2003, Paul Boutros wrote:

> Hi all,
> 
> This is very similar to a question another user asked recently, so I sort of 
> expect the same answer:
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-July/001983.html
> 
> I just received data for a set of 16 Affy chips.  Very unfortunately, the 
> various spike-in controls (e.g. BioB, BioDN, CreX) were only added to half the 
> chips.  We are not entirely clear that those controls are entirely absent in 
> the other half -- a very low signal (10-100) is detected.
> 
> I would like to remove these control probesets at a very early step, so that I 
> can normalize, etc. without this interference.  Is there any way to do this in 
> BioConductor?  Any general suggestions on what else I could do to try 
> to "salvage" as much data as possible from these chips are very much 
> appreciated.
> 
> Sincerely,
> Paul
> 
> 
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