I am performing differential gene expression analysis between to condition of temperature (A and B). I have the matrix of count for all my genes and the 5 replicates for each condition.
And I don't know what to think about it for the continuation of the analysis.
However when I plot the PCA keeping only differentially expressed genes we get better results. But for my part, I think it's a bit biased since it's obvious that genes will cluster between the 2 conditions since we have selected differentially expressed genes ... (whatever the input data would have been)