Dear Mark, Gordon,

 probably a naive statistical question on edgeR : considering 3 samples of
3 library sizes : a) 10 mil reads, b) 30 mil reads, and c) 12 mil reads.

after applying edgeR, I do obtain 1) > 2000 genes differentially expressed
between a) and b) (FDR< 0.01, FC > 2), and 2) only ~ 200 genes
differentially expressed between a) and c) (FDR < 0.01, FC >2).

my question would be : given the fact that the number of differentially
expressed genes is dependent on the library size, would it be valid to
compare and contrast the set 1) of 2000 differentially expressed genes (FDR
< 0.01, FC >2), with an expanded set 2) of 200+800 differentially expressed
genes (FDR < 0.01, BUT FC > 1.2).

thanks a lot,

Bogdan

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