[BioC] gene filtering for limma lmFit
fredyfpeng at ualberta.ca
Fri Oct 16 18:23:30 CEST 2009
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.
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