[BioC] gene filtering for limma lmFit

Peng, Fred fredyfpeng at ualberta.ca
Fri Oct 16 18:23:30 CEST 2009

   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

More information about the Bioconductor mailing list