[BioC] Affymetrix Chips with Missing Spike-Ins

[Paul Boutros]

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


----------------------------------------
This mail sent through www.mywaterloo.ca