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