Hi,

I don't have any reference to give you.

But my experience says that you don't get necessary a good heatmap
separated by two conditions although you use only DE genes. Probably
because many time,s results from DE genes are not so strong to separate the
two groups, or because there is a systematically outlier in your comparison
and get DE genes that are not true, or any other reason.

I can say that I have done more than 50 DE analysis, and only once, I got a
clear heatmap showing two groups. So, I guess there is something there.

very interesting your initiative.

cheers

Lo


On Mon, Dec 9, 2013 at 2:19 PM, Aaron Mackey <ajmackey@gmail.com> 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
>
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