MEgene correlated to triat and Gene signficance coorelated to triat


Hi Biostars ,

I was using WGCNA for co-expression analysis. I used the signed automatic network and module detection method. I have also used "bicor" for the correlation. Everything went well, but I see differences in the number of genes significantly correlated to the trait, and the number of genes in the module-Eigene gene significantly correlated to trait!

In the picture, you see module color salmon and blue have a significant correlation to GIR. These two modules together gave me 2000 genes.

enter image description here
However, when I saw the number of significant genes in the GSPvalue object, the number of significant genes correlated to GIR was 987.

Gene.signif_GIR <-  GSPvalue %>% filterp.GS.IS < 0.05)

I don't know why that happened. I thought it should be the same.

I would appreciate your answers!

Thank you!




updated 2 hours ago by



written 7 weeks ago by



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