Problem with WGCNA - Module-trait relationship
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amoltej ▴ 10
@amoltej-7192
Last seen 6.9 years ago
Australia

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

 

wgcna • 1.9k views
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@lluis-revilla-sancho
Last seen 12 minutes ago
European Union

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

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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

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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?

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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. 

 

 

 

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