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Old 03-08-2012, 11:20 PM   #2
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 993

The division by length is plain wrong. For an enrichment score, you want to divide some measure of signal strength in IP with a measure in CNTL. If your colleagues insist that these measures should be normalized for length, they can do so. However, as both measures are divided by the same length, it cancels out. Incidentally, this is why RPKM is not so useful for differentially expression, either. Dividing by length just obscures how much evidence you have: A ratio of 5 to 2 reads has the same ratio as 500 to 200 reads, but in the latter case you can be more sure that this is a real enrichment and not just chance. This is why the raw number of reads (without normalization) is useful and also why looking at the ratio only is not sufficient.

BTW, are you talking about CLIP, or how come you have IP and control?
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