Hello,

Is there a way in Agi4x44PreProcess to filter out (i.e. change to NA)  
individual flagged signals?
For example, if I do the probe filtering step as in the manual:
ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE,
+ isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE,
+ NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75,
+ limNEG = 75, limSAT = 75, limPopnOL = 75, limNonUnifOL = 75,
+ limNAS = 100, makePLOT = F, annotation.package = "hgug4112a.db",
+ flag.counts = T, targets)
A feature with 5% of signals non-uniform (IsFeatNonUnifOL = 1) will  
pass.  Unless I misunderstand something, this means the 5% of signals  
that were flagged will be included in the processed data set with no  
way to distinguish them. This will affect only a tiny percentage of my  
data but I'd still like to remove those values.

Thanks in advance,
Leslie



*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
Leslie M. Turner, Ph.D.
Payseur Lab
University of Wisconsin
Laboratory of Genetics
Genetics/Biotechnology Building
425-G Henry Mall rm 2455
Madison, WI 53706
Phone: 608-262-6856
Fax: 608-262-2976
email: lturner3@wisc.edu


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