> 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
> 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.
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