Hi, I have for group conditions and I run PCA analysis in DESeq2. After trying different PCs in the PCA plot, I found that PC3 and PC4 plot could well separate my samples: https://ibb.co/d5mpHn
I think that means my signaling probably mainly located in the PC3&PC4 directions, while PC1 and PC2 are just some other un-relevant things. In this case, is there any tricks to let me focus on the signal I wanted? Or is there any papers discussing this issues? I think this phenomenon is quite common in RNA-seq analysis.
Best regards, Raymond