WGCNA can not reach Clusters

Question

[Recep]

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?

Answer 1

[andres.firrincieli]

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

[Recep]

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)

[andres.firrincieli]

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.