[BioC] Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same

[Peter Langfelder]

On Mon, Aug 11, 2014 at 1:26 PM, Sindre Lee <sindre.lee at medisin.uio.no> wrote:

> My thought was that if the module was related weight (in two data sets) and
> changes (log-ratio) in weight, wouldn't that point to a stronger
> relationship? If not, why?

You can think about the log-ratio as conditioning out the denominator
(e.g., time 1 if you do log(time 2/time 1). If you had a strong signal
at time 1, you will take the signal out; if the signal at time 2 was
similar to that at time 1 and you take the time-1 signal out, you're
left with no signal (relating to weight). For gene expressions you're
not only taking out their relationship to weight, you also remove
their correlation at time 1 - if the correlations at time 2 were
similar, you will again be left with data whose correlation structure
is very different from the original, so you most likely won't observe
the same modules again.

Peter