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Old 04-23-2012, 03:35 PM   #1
deepsea
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Default cufflinks --compatible-hits-norm

Hi,

I am testing cufflinks with two different normalization methods: total-hits-norm and compatible-hits-norm. My understanding is that the only difference between these two methods is the FPKM denominator: one is the number of all hits, the other is the number of hits within the reference GTF. So the ratios of FPKM values calculated by two methods should be a single fixed number, which is the ratio of hits. But, the ratios I got is a distribution. Anybody have an idea of the exact meaning of compatible-hits-norm? Thanks!
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Old 04-23-2012, 05:37 PM   #2
sdriscoll
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sounds fishy. i wanna try this out and see what results i get. I'll report back unless of course someone comes in an explains it.
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Old 04-23-2012, 09:39 PM   #3
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Oh I am very sorry! It is my problem: one set was processed slightly differently. :-(

Thanks, sdriscoll!
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Old 04-24-2012, 03:00 PM   #4
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indeed. i tried this today and the difference in FPKM values between the two normalizations was constant out to 4 decimal places.
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