I am using DESeq to detect genes that are differentially
expressed (DE). I am analyzing RNA-seq data from 6 samples, each of
which belong to different class with no biological replicates – this is
a poor experimental design as you noted in the DESeq vignette, but this
is all I have.
What I am finding it to be odd is that the number of DE genes I get from
doing the pair-wise DE detection for 6 samples does not negatively
correlate with the Pearson or Spearman correlation coefficient that I
calculated pairwise amongst these 6 samples (I.e. I expected that
libraries with the higher correlation coefficient would have less number
of DE genes. But this is not what I am seeing.).

I am looking for your insight and was wondering if what DESeq is doing
to detect DE genes may explain what I am observing.

Thank you.


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