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

[Sindre Lee]

On 2014-08-11 23:00, Peter Langfelder wrote:
> 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

Thank you for a nice explanation!

I have to re-think what my approach should be then. I want to find 
weight-related genes and then find out how my intervention effects 
weight through these genes.

So if I want to answer the question "Which genes are changed during 
intervention and associated the change in weight?", what would you 
suggest as an approach?

Thank you again, this has been very enlightening for me.