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Can someone help me understanding the quartile normalization in Cufflinks? I
read different threads in which they reported that the FPKM values were
inflated after normalization (-N) but most people didn't report their values
so I don't know how big the inflation should be...

In my case, the difference is huge! The FPKM values for the four first genes
without normalization are in the range of [61 - 184] while after
normalization, they are in the range of [2.4e+6 - 7.4e+6]. Even though this
inflation does not seem to affect the calculation of the gene expression
changes [ log (FPKM2/FPKM1) ], I'm wondering if something is wrong with my
dataset.

Is it was I should expect? Is it always better to use the normalization?

Thanks,

David
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