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.
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!