[BioC] p.adjust versus decideTests time series

[Urska Cvek]

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I am trying to determine why does the p.adjust return 1944 probe sets but the decideTests returns a different number. I know that I can change the method to "global" on decideTests, but I don't know whether I should be using the "separate" or "global" method in this case. Even when I change to "global" I get a larger number of genes in the intersections and unions, but I still do not get the 1944 as with p.adjust.

Thank you,

U.C. 
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