[BioC] methods for Differential expression

[E Motakis, Mathematics]

Dear all,

I would like to ask which is, at the moment, the most popular method to 
identify differentially expressed genes for two colour cDNA microarrays. Is 
"limma" the method that one would "trust" more in terms of identifying DE 
genes and at the same time obtain a small number of false 
positives/negatives?

Assuming the data are calibrated, do limma (if this is the best method) and 
simple t-test (test of the log transformed intensities) give very different 
results?

Thank you,
Makis




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E Motakis, Mathematics
E.Motakis at bristol.ac.uk