when I using DESeq with my samples(3 replicates each 2 conditions) ,I found that the padj of my final result are always 1. And the pval is normal varying in 0.01-1 .
My complete code are:
cds <- newCountDataSet( countTable, condition )
cds<-estimateSizeFactors( cds )
cds<-estimateDispersions( cds )
res<-nbinomTest( cds, "untreated", "treated" )
I would really appreciate all the advice.Thank you very much.