[BioC] gene filtering for limma lmFit

[Peng, Fred]

   Hello all,
   I  have  a  question  while  I  am using the limma package to identify
   differentially  expressed genes: should I perform gene filtering after
   normalization to exclude genes that are likely unexpressed in the samples
   before fitting the linear model. With my limited stats knowledge, I believe
   the inclusion of 'unexpressed' genes may affect the BH mutliple testing
   correction by unnecessarily increasing the number of genes being tested.
   Previously when I performed global test (using the globaltest package) on
   Affy data, however, I found that the gene filtering step had no noticeable
   effect on the final P-value and therefore had not been required, so I wonder
   if limma's capability to detect differentially expressed genes would be
   affected by whether or not 'unexpressed' genes were filtered out.
   Thanks very much in advance.
   Fred Peng