different numbers of genes for WGCNA and Differential expression

Question

[Gail]

I am working on a project on 62104 genes, and after all the filtering steps in the differential expression resulted to 14642 genes while the WGCNA final dataset used for it had 19669. Now, should the two have equal number of genes? Given that they have different filters? I have looked it up and it said that the Differential expression analysis by edgeR use a more stringent type of filtering. Now I am wondering if I did it wrong because of the unequal numbers.

[ATpoint]

You need to give references and code. Words alone are not helpful.

[allingt]

What are the filtering steps you take in each method and what are your thresholds?

I always find it helpful to visualise or take a note of how many cells/samples/genes are removed after each filtering operation, regardless of the type of analysis to follow.