WGCNA sample number reduction
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anjanaram1 ▴ 10
@anjanaram1-9014
Last seen 18 months ago
United States

Hi,

I have changed my cutoff height to 7. But Im still getting the full list of samples. How do I reduce the samples before I assign them to modules? what exactly is happening in the line:

##datExpr = datExpr0[keepSamples, ] 

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#### Plot a line to show the cut
abline(h = 7, col = "red");
#### Determine cluster under the line
clust = cutreeStatic(sampleTree, cutHeight = 7, minSize = 10)
table(clust)
#### clust 1 contains the samples we want to keep.
keepSamples = (clust==1)
datExpr = datExpr0[keepSamples, ]
nGenes = ncol(datExpr)
nSamples = nrow(datExpr)

wgcna networkanalysis • 156 views
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What is the max height of tree and what is the max size of cluster?

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