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Old 05-20-2014, 04:09 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Don't use any of the options you presented. You absolutely want to use the replicates as replicates to better gauge biological variability. You'll be using one of the normal RNAseq packages (DESeq2, edgeR, limma, etc.), which can handle replicates natively. The problem is actually the comparison of unreplicated samples, for which the results will be questionable.
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