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Old 05-18-2011, 01:57 AM   #1
Location: Japan

Join Date: Oct 2010
Posts: 52
Default DESeq: question about replicates

One question about replicates in DESeq.

I read "Analysing RNA-Seq with the DESeq package", version from April 21, 2011.

In the "Quick Start" section of abovementioned document, they strongly advice to sum-up "purely technical" replicates and have only biological replicates in separate columns. However, in my experiment it's not clear to me if some of the replicates are "purely technical" or rather biological: I am analyzing different brain tissue samples in treated and untreated states. I have samples where the RNA-preparation has been done in duplicate from the same biological tissue, then sequenced independently. Is this to be considered technical or biological in the context of DESeq?

Last edited by Azazel; 05-18-2011 at 07:25 PM. Reason: Originally this post contained two unrelated questions about DESeq. I now split this into two. Answers below still in context
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