Downstream analysis#

Differential Expression#

Differential expression for count data can be determined, downstream of the pipeline, with count based DE packages such as edgeR and DEseq. We do not recommend however using the output of mmseq and cufflinks with these methods. Users should instead provide their own test, of which t-tests or likelihood ratio tests would be suitable examples.

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« This page (revision-8) was last changed on 10-Jul-2014 13:18 by Andrew Tikhonov