Question: Can I use a matrix of Pearson Correlation Coefficients as input into WGCNA?
gravatar for maureen.pittman
3.9 years ago by
United States
maureen.pittman0 wrote:


I am using public expression data to create weighted co-expression networks in WGCNA. One source I was hoping to use (COXPRESdb) has aggregated expression data in the form of Pearson correlation coefficients calculated for all pairwise comparisons of gene-expression values. Would this matrix be valid input into the WGCNA pipeline?

Specifically, I'm not sure if I could use this matrix to choose a soft thresholding power as outlined in the manual, since it is assumed the starting point is a matrix of gene expression across samples. I also don't know whether the adjacency() and TOMsimilarity() functions should be used on a matrix of gene-pair correlation values instead of the sample matrix. Does it make sense to use this kind of processed data in WGCNA?

Thank you,


ADD COMMENTlink modified 3.3 years ago by Lluís R.890 • written 3.9 years ago by maureen.pittman0
gravatar for Lluís R.
3.3 years ago by
Lluís R.890
Spain, Barcelona
Lluís R.890 wrote:

This is a bit old but since is quite viewed I answer it.
You can use it, this is called in the package similarity matrix, to select the soft thresholding power you can use pickSoftThreshold.fromSimilarity, there are similar function to calculate adjacency

ADD COMMENTlink written 3.3 years ago by Lluís R.890
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