[BioC] limma and gpr flags?

[Simon Melov]

I have been flagging various spots in gpr files for qc reasons in 
genepix, and they are appropriately given a negative number in the gpr 
file. However, after reading in the gpr files via the following, 
carrying out analysis as described in the limma guide, and generating a 
list of the top 100 DE genes via Bayes, I am still getting flagged 
genes in the final output.

Shouldnt these be excluded from the entire analysis by the wt.fun?

files <- dir(pattern="*.gpr")
RG <- read.maimages(files,source="genepix",wt.fun=wtflags(0.1))


thanks

Simon.
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