hi,

A few papers have concluded that DESeq is more accurate for DE genes
discovery than methods using FPKM, and that the bias in FPKM is that a
gene’s FPKM depends on the expression of other genes due to the division by
library size.

Now if my purpose is for visualization or analysis other than looking for
DEGs,  I wonder if it’s better to replace FPKM by DESeq normalized gene
count divided by gene length?


Thanks for your comment!


Jack

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