Patterns within groups with RNA-seq

Question

[gaiusjaugustus]

I have RNA-Seq data from patients with different stage cancer, and have done a differential expression analysis comparing stages to each other and stages to normal tissue.

However, what I'd like to do is look for expression signatures WITHIN one stage (late stage) of the cancer.

Any suggestions for the best way to do this?

Thanks in advance for any help.

Answer 1

[Hussain Ather]

Is there a way to divide up the late stage into different categories and find the differential expression between them?

[gaiusjaugustus]

Yes, there is. I could divide it by certain covariates (survival, mutated genes, etc). But I want a more machine learning (clustering) sort of way that isn't limited by the covariates that I have available or think of.