A colleague of mine is skeptical of my assertion that drawing sample-level
PCA plots and/or clustered heatmaps based only on differentially expressed
genes (DEGs) is a circular, self-fulfilling prophecy -- they assert that
there's no guarantee samples will cluster by condition (despite the fact
that the condition is exactly what drives selection of DEGs), and so hopes
to use the observed clustering as further "evidence" of the condition
effects.  Rather than spend more time trying to explain statistical
concepts, I was hoping to checkmate the argument with a nice Nature Methods
review or somesuch.  Any pointers?

Thanks in advance,
-Aaron

	[[alternative HTML version deleted]]

