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Old 02-05-2013, 11:43 PM   #1
drKM
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Location: Taiwan

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Default Normalization methods in cuffdiff 2.02

Hi there,

I'm a newbie using cuffdiff.
Could anyone explain the three methods in cuffdiff to me?

1. raw-mapped-norm
2. geometric-norm
3. upper-quartile-norm

And which one should we use in what situation or could use them jointly?
The manual only described about 'upper-quartile-norm :With this option, Cufflinks normalizes by the upper quartile of the number of fragments mapping to individual loci instead of the total number of sequenced fragments. This can improve robustness of differential expression calls for less abundant genes and transcripts.'

Thanks for any words.
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