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.

I posted an answer here:

A: deseq: all padj values equal to 1