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WGCNA can not reach Clusters

Hello,

i have clustered my genes through this tutorial.

I want to correlate each these clusters with disease scores. Though i cant find my clusters as a dataframe.

How can I find the dataframe showing the genes and the clusters they belong to?

wgcna
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updated by andres.firrincieli andres.firrincieli • written by Recep • Recep

1 answer

I want to correlate each these clusters with disease scores. Though i cant find my clusters as a dataframe.

You first calculate the module (cluster) eigengenes (MEs) with

MEs = moduleEigengenes(datExpr, moduleColors)$eigengenes

Then use the MEs to calculate the correlation values and significance with the disease score

moduleTraitCor = cor(MEs, datTraits, use= "p") # calculate the correlation (pearson)
moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples) # calculate the pvalues

If you do not understand what the MEs are, read the paper

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written by andres.firrincieli andres.firrincieli

Thank you! yes i understand, but i dont want to correlate with pearson, but linear mixed models. So i just need the clusters.

Therefore i need a code like:

mixed.lmer <- lmer(MEs ~ DiseaseScores + (1|df$PatientID_x), data = df)
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written by Recep • Recep

Hi Recep,

sorry for the late reply. To subset the expression matrix of each module from the original datExpr you could use the following chunck of code:

datExpr_blue<-datExpr[,moduleColors=="blue" ] # to extract the expression matrix of the blue module

edit: I would run the lmer only for modules that show significant correlation with the DiseaseScores.

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written by andres.firrincieli andres.firrincieli

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