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Old 03-11-2012, 10:28 AM   #3
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Location: New York, NY

Join Date: Mar 2012
Posts: 2

Yes, this is for a form of IP. So I'm trying to gauge the enrichment of the IP over the control in a given window. I've heard that RPKK is apparently not a good measure anymore, and that length normalization actually increases variance, so I agree with your point there.

So we've opted to just use a read count ratio, normalized by total number of reads mapped in IP/control, respectively. Using Fisher's exact test produces too many p-value counts of 0s, because the enrichment is too high to be quantified with the test.

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