|Thread||Thread Starter||Forum||Replies||Last Post|
|Should one combine normalization methods in RNA-seq?||BGould||Bioinformatics||2||07-20-2016 12:32 PM|
|identical results from different normalization methods in cuffdiff v2.0.2?||discrim||RNA Sequencing||0||09-21-2012 01:30 AM|
|PubMed: Comparison of Normalization Methods for Construction of Large Multiplex Ampli||Newsbot!||Literature Watch||0||04-27-2010 03:00 AM|
|02-05-2013, 11:43 PM||#1|
Join Date: Sep 2012
Normalization methods in cuffdiff 2.02
I'm a newbie using cuffdiff.
Could anyone explain the three methods in cuffdiff to me?
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.