Dear Dr. Anders,

Hello. I am comparing the differential expression tools.  For my data set,
there are two samples with no replicates. For DESeq, since I am doing the
multiple test, I think I should use adjusted p-value rather than p-value.
However if I choose adjusted p-value, there are only 152 genes left out of
23360 genes excluding NA, since for 20861 genes, they have p.adj=1. Even
there are only 49 genes for pval<0.05. One of the tools I am comparing with
DESeq is edgeR. If I use pval in DESeq to compare, it works pretty well,
and I can see there are many common genes (around 80%) in these two
packages. However, since the default p-value in edgeR is adjusted p-value
with BH method, I am not sure I can use p-value. How can I solve this
problem? Please let me know. Thank you for your in advance.

Best regards,
Lucia

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