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

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/00198 3.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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >