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Old 02-20-2014, 10:38 AM   #2
Michael Love
Senior Member
Location: Boston

Join Date: Jul 2013
Posts: 333


I think what you want to use is the likelihood ratio test. You can either do this with DESeq():

dds <- DESeq(dds, test="LRT", full=~stage, reduced=~1)

or you can also use the nbinomLRT() function:

dds <- nbinomLRT(dds, full=~stage, reduced=~1)

The likelihood ratio test compares the difference in log likelihood using the stage information vs removing the stage information altogether. This then gives you a significance test for whether the gene expression changes with stage, at any point in the life cycle like you say.
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