Hi,

I am analizing a set of microarrays with SAM strategy using SIGGENES
package. The microarray data is the following:

Name Description

FLAG <- 7 arrays of an IP over RNA from a transgenic animal with a TAG in
the protein of interest for the IP
Wt <- 7 arrays of an IP over RNA from an Wild type animal
WAFLAG <- 3 arrays of total RNA from the Whole Animal  with a TAG in the
protein of interest
WAWt <- 3 arrays of total RNA from the Whole Animal

I am interested in those transcripts that are significatively change in
FLAG vs Wt samples, as those transcripts would be the hipothetical targets
of my protein of interest. However, I would like to avoid noise from the
FLAG epitope of my protein in the total RNA samples. To these end, I
compared WAFLAG vs WAWt samples.

So, here is my problem. I am not sure what to do in order to avoid the
noise I described above. What I was thinking is to substract the fold
changes generated in WaFLAG vs WAWT to the expression values to the FLAG
and Wt samples before make the SAM analysis over these FLAG and Wt. Also I
don´t know if there is a way to construct in some way the CL vector in
siggenes. Any suggestions will be highly appreciated. Another thought I
have, is that only a have to worry about those genes that significatevely
changed in both contrasts, WaFLAG vs WAWT and FLAG and Wt.

Mark

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