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

[Peter Langfelder]

Hi,

the correlations are different because the two functions, which are
just visualization functions, visualize different relationships. In
the heatmap you see correlations of module eigengenes with the trait,
while the verboseScatterplot probably shows the scatterplot of
individual gene signifcances vs. their module membership. Hence the
number of observations in the heatmap is your number of samples,
whereas in the scatterplot the number of observation is the number of
genes in your module, which is typically larger.

HTH,

Peter

On Fri, Aug 8, 2014 at 4:40 PM, Sindre Lee <sindre.lee at medisin.uio.no> wrote:
> Hello!
>
> I have used the WGCNA package and found 2 modules which are of interest for
> me. I picked out from the labeledHeatmap (which related the module eigengene
> with clinical traits). I then selected the modules (one at a time) and ran
> the verboseScatterplot function.
>
> For one module its correlation was 0.51, p = 0.01 in labeledHeatmap, but
> 0.27, p<0.0001 in the verboseScatterplot.
> How can this be?
>
>
>
> Thank you.
>
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