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Old 04-10-2014, 06:38 AM   #4
TheSeqGeek
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Location: USA

Join Date: Feb 2014
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Quote:
Originally Posted by NicoBxl View Post
use DESeq or edgeR ( in R ) to normalize and check for DE genes
I use DESeq2 and I print out the normalized values then do a ttest of my own but my pvalues are nothing like in DESeq2.

I use this code to print out normalized values.

normalizedCounts <- t( t(counts(dds)) / sizeFactors(dds) )
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