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Old 06-08-2010, 04:46 AM   #1
sanush
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Location: san diego

Join Date: Nov 2009
Posts: 14
Default DE calculation for RNA Seq

Hi all
I am analyzing RNA seq data for DE. We have 2 groups (control & treatment) and sample in each group. We have calculated the RPKM values but not sure how to calculate the Fold change between groups. I was trying to find ratio using the RPKM values but we find huge up or down regulation when the rpkm values between the group are extreme values. Here is an example

Control Treated Ratio
Gene A 1.82836 2.57E-09 = 1.41E-09

In this case the read count for the treatment count is very low when compared to the control. I am not a bioinformatics person so maybe someone could help explaining how to calculate the FC.

Thanks in advance
Sanush
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