When DESeq is used for our RNA-Seq data analysis of two conditions, each of
them has three biological replicates, we got a result better than Cuffdiff2
and CLCBio Genomics Workbench, verified by RT-qPCR.

Based on the normalized counts and adj-p values, can we also tell with
confidence which genes are highly expressed and which genes are rarely
expressed within the same conditions.  I knew that DESeq have library size
factor in normalization, but do not have gene length factor in
normalization like Cuffdiff2.  Any comment will be highly appreciated.

Chun

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