Search
Question: Problem with WGCNA - Module-trait relationship
0
gravatar for amoltej
9 months ago by
amoltej10
Australia
amoltej10 wrote:

Hello everyone, 

I am trying to run the WGCNA on my data set of 87 samples. 

First 2 steps executed successfully. In the third step when running following commands I am getting all the "NA"s in the output.

moduleTraitCor = cor(MEs, datTraits, use = "p")
moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples)

please find input files for these commands below

MEs0 - https://drive.google.com/open?id=0B42oFSm-XOAUbm9fRkx2Qk8wNDQ

MEs - https://drive.google.com/open?id=0B42oFSm-XOAULTEtcHdSWUMtQ0k

Can someone please help to understand whats happening.

thanks in advance

 

ADD COMMENTlink modified 9 months ago by Lluís R330 • written 9 months ago by amoltej10
0
gravatar for Lluís R
9 months ago by
Lluís R330
European Union
Lluís R330 wrote:

The first line calculates the correlation of each trait with the egienvalue of each module, the second line gives you the p-value of said correlations for a given number of p-values. I advise you to use a function named somehow like corAndPvalue which gives both correlations and p-values takeing into account the number of samples with information for each trait

ADD COMMENTlink written 9 months ago by Lluís R330

Hi Lluis, 

Thanks for the reply but the result is still same. I suspect for some reason correlation is not calculating or calculating it to 0 for all the values

ADD REPLYlink written 9 months ago by amoltej10

What code do you use for "the third step"? Are there any NA in your input data? Did you use the "complete" observations option to calculate the correlations?

ADD REPLYlink written 9 months ago by Lluís R330

I am using this code for third step - https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-03-relateModsToExt.pdf

Yes, I am using complete observations to calculate correlations. There are no NA's in the input dataset for these commands. you can check input files from my question. 

 

 

 

ADD REPLYlink written 9 months ago by amoltej10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 315 users visited in the last hour