Question: WGCNA trait question
gravatar for joetaylor268
23 months ago by
joetaylor26810 wrote:

Hi there

I have a large RNAseq dataset where the expression of about 20,000 genes is determined for various different B-cell populations. I have performed WGCNA and have identified consensus modules using all conditions.

My next task is to see how these modules correlate with 'traits' (module-trait relationship) and to display these correlations in a heatmap, to identify which modules are associated with the various B-cell types.

Now comes my problem. can I use the gene expression values for the different B-cell categories as trait data? I have tried using the following code:

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

labeledHeatmap(Matrix = moduleTraitCor, xLabels = rownames(datTraits), yLabels = names(MEs), ySymbols = names(MEs), colorLabels = FALSE, colors = blueWhiteRed(50), textMatrix = textMatrix, setStdMargins = FALSE, cex.text = 0.4, zlim = c(-1,1), main = paste("Module-trait relationships"), cex.lab.y = 0.5)

the problem is that I have generated a heatmap displaying correlations for module eigengene values with expression level for ALL genes - I want to see the correlation between module eigengene values for the different B-cell groups

How can I do this?

rna-seq next-gen genome • 1.5k views
ADD COMMENTlink written 23 months ago by joetaylor26810
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

How do you define a B-cell group?

ADD COMMENTlink written 23 months ago by Kevin Blighe63k

My RNAseq expression matrix provides gene expression values for all genes for different B-cell subtypes - so germinal centre B-cells, Marginal zone B-cells, Follicular B-cells etc. matrix = rows (genes) x columns (B-cell group)

ADD REPLYlink written 23 months ago by joetaylor26810

You can correlate the module eigengenes to anything, whether continuous or categorical. If you want to correlate to a group of genes at the same time, you will have to come up with a summary metric for those genes.

ADD REPLYlink modified 16 months ago • written 23 months ago by Kevin Blighe63k
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