joey711/phyloseq-extensions — pull request #1 by chuckpr (2014-06-25 17:30:03+00:00)
Title: set cooksCutoff to FALSE in results function call

I think the NA p-values are due to the Cook's distance filtering in DESeq2. When you set "cooksCutoff" to ```FALSE``` in the ```results``` function call, the p-values show up.