How to do unsupervised clustering of RNA-Seq data

Question

[Kumar]

Hi, I have got count matrix of the RNA-Seq data (total 187 samples) using STAR and featureCounts. Here are the factors of the data: (affected: male and female and unaffected: male and female). And used DESeq2 package for DGE analysis. In the result, I have got 679 differential genes expressed with 0.05 p-value. Now I am looking to make clusters of the data according to the factors (affected: male and female and unaffected: male and female). Please suggest any approach or script.

[Renesh]

You can try PCA https://reneshbedre.github.io/blog/pca_3d.html and heatmap with hierarchical clustering https://reneshbedre.github.io/blog/hmap.html

[Kumar]

Hi, Thank you for your reply. I have made PCAs after transformation vsd and rld. But these seem mix-up all the samples. I need to make these in different groups to see the clear cluster. Please let me know if you have an idea.