> I am wondering why Cuffdiff suddenly gives many more significant DE genes?

Cuffdiff was recently updated to version 2.1.0; this update likely explains the 
different results that you see.

> I have rerun several analysis, also with more samples in each group, all give 
> much more significant genes. Why?

More samples = more power to accurately estimate expression levels = more DE 
genes.

> Also, will replicate information soon be included in output files?

Replicate data will be available when we next update our server. This should 
occur in about 3 weeks.

Best,
J.

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