I have a RNAseq data set with 10 samples. I noticed that I get slightly different fpkm values when I use colSums and sizeFactors for read count normalization. (See the following figure for )
My question is how to figure out which library size data use use for normalization? Does it depend on the personal preference?
Really appreciate your comments on this.
Thank you very much you all for the material. This is very helpful!