Hi, I have 74 cancer cases who their RNA-seq gene expression belongs to 14 batches. My exprData was normalized by FPKM method. After running
prcomp() on my expression data, I plotted
PC2. my plot is available in this link. Now, I need to know more about the interpretation of that plot. does my exprData has batch effects? does it need to batch effect correction?
I appreciate it if anybody shares his/her comment with me.