Question: scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"
4.0 years ago by
Aaron Mackey • 200
Aaron Mackey • 200 wrote:
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]]
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