Thank you! I understand now, its actually well described on the
and in the documentation, I should have used more time reading before
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
2. Is it always better to use the step-by-step network construction
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
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
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
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:
> 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
> 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
> genes in your module, which is typically larger.
> On Fri, Aug 8, 2014 at 4:40 PM, Sindre Lee <sindre.lee at="" medisin.uio.no="">
>> 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
>> 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
>> 0.27, p<0.0001 in the verboseScatterplot.
>> How can this be?
>> Thank you.
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> Search the archives:
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives:
Medical Research Student
Department of Nutrition, Institute of Basic Medical Sciences, Faculty
of Medicine, University of Oslo
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E-mail: sindre.lee at medisin.uio.no;
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