I have a question, I get no significantly changed genes running DESeq2. I have two groups at two time points (paired) and ran DEseq2 v1.2. DESeq2 test the difference between groups, disregarding time point, difference between time points disregarding groups & finally if one group had another effect between the two timepoints than the other.
I have also used Cuffdiff 2.1.1 testing difference between groups, disregarding time point & difference between time points disregarding groups (Cuffdiff cannot handle the last test).
Cuffdiff found over 1000 diff exp. genes and running GAGE it all made biological sense. So why cant I find anything with DEseq2?
I have also used Cuffdiff 2.1.1 testing difference between groups, disregarding time point & difference between time points disregarding groups (Cuffdiff cannot handle the last test).
Cuffdiff found over 1000 diff exp. genes and running GAGE it all made biological sense. So why cant I find anything with DEseq2?
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