Hi,

I have been using Limma for analysing my GenePix data.  As described in the
Limma user guide, I use the wt.fun to set 0.1 weight to all the flagged
spots. I understand that these flagged spots will not be used for
normalization purpose. My question is: Are these flagged spots considered
for calculating P values or adjusted P values?  If so, is it a good idea to
remove those flagged spots before doing linear fit?

Thanks in advance.

Best regards,
Sharon

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