Dear all,

I am analyzing RNA-Seq data and am interested in investigating genes involved in sexual dimorphism in nematodes. I have differential expression data (15k genes) in FEMALEvsMALE conditions, each with two replicates (drf1, drf2) for FEMALE and (drm1, drm2) for MALE. I have been exploring the WGCNA package in R to obtain gene co-expression networks and advance in my analysis. However, to do this, I need at least 15 samples. My question is:

Is it possible to perform this analysis with WGCNA? What analysis would you recommend to address my research question?

Thank you!

Is it possible to perform this analysis with WGCNA?

WGCNA is not a Bioconductor package. Anyway, the developers are not trolling you by recommending > 15 samples. It's correlation-based and with only n=2 and two groups, so n=4 total, there is no power.

What analysis would you recommend to address my research question?

It's off-topic here. You can ask at biostars.org for suggestions but for this you need to add details what question you want to answer.