[BioC] SAM vs LIMMA vs EBAM

[Wu, Xiwei]

Hi, BioC Members,
 
I have a general question on identifying DE genes. Since there are many ways
to do this, I am wondering whether people has compared methods such as SAM,
EBAM, and LIMMA by applying them to the same dataset. Of course, they have
different assumptions and different models, but should they always give
similar results (assuming the parameter settings are optimized to get
similar number of DE genes)? Is it better to get a common list of genes
using three different methods? Do I have more confidence on this common list
of genes than using a single method?
 
Xiwei
 

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