I am analysing RNASeq data. I got 45 samples with nine different treatment, each five replicate. 9*5 = 45 (experimental design).
I did PCA and they do not seem to separate quite well based on treatment. pc1 = 12 % pc2 = 10 % pc3 = 7 %
I did pairwise differential expression among the samples. And I am planning to do PCA on DE genes only. I have normalised matrix of all the genes. My question is:
To do PCA on selected gene should I take input of all genes normalised -> correlation matrix -> retrieve DE genes only -> prcomp
OR from normalised gene matrix -> retrieve DE genes -> correlation matrix -> prcomp
Any help would be much appreciated. Thanks