[BioC] lmFit, weights and A

[lepalmer at notes.cc.sunysb.edu]

I was playing around with weights and examining the results.   I changed 
the wieghts prior to doing duplicateCorrelation,lmFit,eBayes and topTable 
in limma.  Changing all weights to 1 (were previously they were 1 or 0) 
had  a dramatic affect on M values, but did nothing to A.    Is this 
intended?  I would think that if you flagged something, you would not want 
the results included in the calculations for A.

-Lance Palmer
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