Cufflinks quantification and Cuffdiff output
Hello!!!
I used Cufflinks for quantification and for differential expression analysis but I have an important question:
I obtained FPKM quantification values for each sample like this:
tracking_id FPKM1 FPKM2 FPKM3
XLOC_000007 1.19211 0.858113 1.06576
but when I compare this 3 sample with Cuffdiff the relative FPKM value are very different and higher
tracking_id FPKM1 FPKM2 FPKM3
XLOC_000007 311.493 276.814 230.429
why?
I used Cufflinks for quantification and for differential expression analysis but I have an important question:
I obtained FPKM quantification values for each sample like this:
tracking_id FPKM1 FPKM2 FPKM3
XLOC_000007 1.19211 0.858113 1.06576
but when I compare this 3 sample with Cuffdiff the relative FPKM value are very different and higher
tracking_id FPKM1 FPKM2 FPKM3
XLOC_000007 311.493 276.814 230.429
why?