Question: WGCNA - stable Gene clustering
gravatar for ly.leifels
2.7 years ago by
ly.leifels0 wrote:

I have a sample dataset derived from single cell RNA Sequencing with 1800 samples. Some genes have only few counts. Using WGCNA I can compute modules and even define the module membership for each gene for each module. I want to find the number of counts for which a gene would be safely clustered into a module. Would it be valid to: Define genes with counts e.g. lower 5, by computing the max(counts) for each gene in the original dataset and select gene names. Create subsets with 80% the original dataset counts and compute the module membership in each subset. Compare module labels between subsets for groups of genes (counts lower 5, counts >5 and <10, and so on..) and select the group for which the module label doesn't change? What would be a more statistically valid way to compute module membership preservation for genes?

wgcna • 864 views
ADD COMMENTlink modified 2.7 years ago by Lluís R.890 • written 2.7 years ago by ly.leifels0

Hello ly.leifels!

It appears that your post has been cross-posted to another site: (and answered there)

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.7 years ago by WouterDeCoster43k
gravatar for Lluís R.
2.7 years ago by
Lluís R.890
Spain, Barcelona
Lluís R.890 wrote:

The number of counts don't decide if a gene would clustered into one module or another. To set a gene in a module or in another what it is important (for WGCNA) is if the correlation between the genes is high.

To calculate the cluster preservation there is a function (modulePreservation), as well as several tutorials.

ADD COMMENTlink written 2.7 years ago by Lluís R.890
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