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

[Sindre Lee]

Thank you! I understand now, its actually well described on the webpage 
and in the documentation, I should have used more time reading before 
posting.

If you have the time, I actually have a few more questions:

1. Why is the module size set at min. 30? What will the implications be 
if larger/smaller?

2. Is it always better to use the step-by-step network construction and 
module detection? Let me give you some details of my design so you 
understand why I ask. I have two time points, from the same persons, 
before and after an intervention. My immediate idea was to run WGCNA on 
the time point 1, relating it to body weight. Then I run WGCNA on time 
point 2, seeing if the same modules pops up. Finally, I run WGCNA on the 
log-ratio ( time point 2- time point 1 ) against log-ratio of body 
weight. If one or more modules shows up in all three runs, they will be 
prioritised. Now, if I only use the one-step approach, no modules show 
up in all three comparisons, while using step-by-step looks more 
promising. However, if I mix the results, using one-step on time point 
1, but step-by-step on time point 2, its even more interesting.

Thank you very much!



On 2014-08-09 18:30, Peter Langfelder wrote:
> 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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-- 
Best regards

Sindre Lee
Medical Research Student

Department of Nutrition, Institute of Basic Medical Sciences, Faculty 
of Medicine, University of Oslo
POB 1046, Blindern, 0317 Oslo, Norway
Visiting address: Sognsvannsveien 9, Domus Medica
Mobile phone: +47 46796851
E-mail: sindre.lee at medisin.uio.no;
Web page: http://www.med.uio.no/imb/personer/vit/sindrle/index.html