Scale independence and Mean connectivity in WGCNA?
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2.3 years ago

Hi,

I am trying to find the co-expression in my RNA-Seq data (Control vs Treatment) using WGCNA. But I am getting some weird plot for Scale independence and Mean connectivity and based on that how can i select the soft threshold.

Thankyouenter image description here

R Plot WGCNN • 996 views
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what is the output of

dim(datExpr) # I am supposing that your expression matrix is called datExpr
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Hi Andres, My expression matrix is input_mat

> dim(input_mat)
[1]    6 2243
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You can't run wgcna with just 6 samples. You will need at least 15 samples

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Thankyou so much

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