[BioC] lmFit, weights and A

[Sean Davis]

On May 18, 2005, at 4:18 PM, lepalmer at notes.cc.sunysb.edu wrote:

> 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.

The A values do not enter calculations of duplicateCorrelation, lmFit, 
eBayes, or topTable, as far as I know.  They are reported in topTable, 
yes, but A values don't affect which genes show up as differentially 
expressed.  Is there a specific reason you want to know the "weighted" 
A-values--just curious?

Sean