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Aaron Mackey
▴
200
@aaron-mackey-3833
Last seen 9.9 years ago
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
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