[BioC] FDR adjustment in LPE

[Jain, Nitin]

Hi,

In a recent paper submitted to BMC bioinformatics, we show that resampling
based FDR 
adjustment method is better than BH method for small sample size. For small
sample sizes, 
BH is quite conservative as shown in our simulation study.

Will put the copy of the submitted paper at:
http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/Sof
tware/LPE/index.cfm

Best,
-Nitin

______________________
Nitin Jain, PhD
Non Clinical Statistics
Pfizer, Inc. (Groton, CT)
Bldg: 260, # 1451
Ph:  (860) 686-2526 (Office)
Fax: (860) 686-6170



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of
jean-louis.ruelle at gskbio.com
Sent: Monday, May 23, 2005 8:52 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] FDR adjustment in LPE



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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