[BioC] limma,weights & fit

[daniela marconi]

Hi limma users!
I have two quick questions
1)I know that setting  wt.fun=wtflags(0) in read.maimages() exclude flagged spots from normalization. But does it exclude flagged spots also from the fitting of linear model in lmFit()?

2)Is it possible that setting a different value (for example like wt.fun=wtflags(0.1) ) make p-value worse and also change the vastly the ID in the topTable() list?
Thanks for any suggestion
Daniela