[BioC] Following meta-analysis, how to address type 2 error?

Ochsner, Scott A sochsner at bcm.tmc.edu
Tue Jul 1 20:03:04 CEST 2008

Dear BioC,

I've been using a weighted Stouffer method to combing p-values (one-tailed) derived from multiple microarray experiments performed in independent labs.  Each experiment roughly address the same null hypothesis:  addition of receptor ligand for 24h has no effect on gene expression.  I have then taken
the combined Stouffer z-score and transformed it back to a two-tailed p-value followed by FDR correction to address Type 1 errors.

I would now like to address the likely magnitude of Type 2 errors.  Unfortunately I'm not in a position to do any wet bench experiments to validate a randomly selected subset of the data points. I would be grateful if someone could direct me to a suitable correction or method which might help to get
a handle on the type 2 error involved when doing thousands of weighted Stouffer calculations. 

Scott A. Ochsner, Ph.D.
NURSA Bioinformatics
Molecular and Cellular Biology
Baylor College of Medicine
Houston, TX. 77030
phone: 713-798-6227 

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