Clustering Challenges in Gene Expression Analysis Using WGCNA

Question

[NDA]

Hi, I am currently analyzing a dataset that includes gene expression data from approximately 400 patient and control samples. My objective is to run WGCNA on this dataset. To enhance the analysis, I aim to identify the most variable genes using the CV (coefficient of variation) parameter. However, I have encountered a challenge: the variability among the genes is substantial, with a minimum CV value of 0.1116, a maximum of 999.2749, and a mean of 0.6288. Consequently, the clustering results of the samples have not yielded satisfactory outcomes. I would appreciate any guidance or recommendations on how to address this issue. Thank you.

[andres.firrincieli]

Consequently, the clustering results of the samples have not yielded satisfactory outcomes.

Could you elaborate?