[BioC] FDR adjustment in LPE

[jean-louis.ruelle at gskbio.com]

Hi all,

The LPE (Local Pooled Error)   package has 2 methods to compute the FDR 
correction for multiple testing : the Benjamini-Hochberg (BH) method, and 
the resampling based FDR adjustment.
Can somebody advise me on which one to choose ? Is one always the best, or 
does it depend on circumstances, like the sample size or something else ?
In a test run of two 2 groups and 3 samples/group, the resampling method 
gives 2x more differentially expressed genes than the BH method, at 
FDR=1%.

Jean-Louis

====================================================
Jean-Louis Ruelle, PhD
GlaxoSmithKline Biologicals, R&D
Rue de l'Institut, 89
1330 Rixensart
Belgium

Phone : + 32-2-6568451
Fax :   +32-2-6568436
email :  jean-louis.ruelle at gskbio.com

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