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Old 05-18-2011, 02:30 AM   #2
Location: Sweden

Join Date: Nov 2009
Posts: 83

Originally Posted by Azazel View Post

2.) 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?
The answer to this shouldn't have anything to do with DESeq - it's the same issue regardless of the software used. I would say the answer lies in part of your question
in duplicate from the same biological tissue
To me it is then clear - this is a technical replicate and it would be wrong to classify those duplicate sample preps as independent biological replicate as they are from the same individual.
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