[BioC] limma and Rank Products: comparison of the number of results

[Juan Carlos Oliveros]

Dear all

When working with comparative experiment based on Affymetrix gene 
expression arrays I usually apply one of the following combination of 
methods:

RMA + limma + FDR

or

RMA+ Rank Products
(rank products "Percentage of false prediction" values are supposed to 
be equivalent to FDR)

Usually we obtain much more differentially expressed genes when using 
Rank Products than when using limma at the same FDR threshold.

I wonder if in your case is the same. Do you obtain many more results 
with Rank Products than with limma at the same FDR cutoff?

In a recent experiment we obtained the opposite (more results with 
limma) and I'd like to know your experience when using both methods 
regarding the number of results.

best,

Juan Carlos Oliveros, Ph.D.
CNB-CSIC, Madrid, Spain