Hi all
I apologise for what may be a very stupid question, but I am currently trying to interpret my WGCNA results, and I could not find anything online about what the following means.
I am interested in this module turquoise (Module-trait relationship table). There is a fairly weak correlation between this module and traits "3" and "6". However, when I plot gene significance (the degree of association between genes in the turquoise module with traits 3 and 6) vs module membership (the degree each gene is associated with these modules), I get very dissimilar degrees of association.
For example, for trait 3, there really is nothing there (as expected, based on the trait-relationship association described on the table). However, for trait 6, there is a strong correlation between GS and MM - but why is this not reflected on the trait/module correlation calculated in the trait-module relationship table (link above)? Is WGCNA correcting for something else when the table is calculated?
I hope this makes sense!
Thanks!
For trait 6 I do not see anything wrong.
None of the hub genes (genes with the highest module membership) in the turquoise module show a strong correlation with the trait 6. Also, the majority of the genes in the turquoise module show a correlation (pearson) < 0.1 with that trait:
This explain why the Module eigengene (1st Principal component) of the turquoise module poorly correlate with the trait 6 (Module-trait relationship table).
Perhaps, I would plot the heatmap of each module to see if the gene expression in your modules is in agreement with your experiment design. I suppose that the gene in the turquoise module are co-expressed only in few samples
To plot the heatmaps, try this:
Dear Andres,
I have a similar question also regarding the difference between Module-trait correlation and GS - MM correlation. I strugle understanding what exactly these numbers represent and why are they so different.
In example, in my yellow module, for my trait DG_brain_region I have module-trait correlation == - 0.8 (pval = 3e-05) but when I plot GS vs MM for this trait in module yellow I get cor=0.51, p = 2e-37.
This module is highly correlated with another brain region CA3 - according to module-trait heatmap correlation is 0.69, pval = 9e-04. When I plot GS va MM, I get cor=0.34, p = 3.3e-16.
So frrm the scatterplots it looks like yellow module is actually more corelated with DG and not with CA3 while the heatmap shows the opposite. Or do I misunderstand the plots?
Could you please explain why these values are so different?
Hi Anna,
Are you working with a signed or unsigned network? Can you show the heatmap of the yellow module?
Hello, sorry for my late response. this is the heatmap:
https://drive.google.com/file/d/165fizcsWcA2uzRPVV2cKNPOcqM1d2WfG/view?usp=sharing
I also have another very similar question, I posted it here: Calculation of module membership in WGCNA