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Old 07-19-2011, 07:34 AM   #1
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Location: Bristol, UK

Join Date: Jul 2011
Posts: 6
Default Differential expression from RNA-seq: variation between replicates


Iím trying to figure out a method for analysing some RNA-seq data (and Iím very new to this so simple wording please!). I have 2 groups, each with 3 replicates. I want to:

1. assess the variation in expression between 3 replicates, then
2. assess the differential expression between the 2 groups (pooled data from the 3 replicates), taking the into account the variation between the replicates to minimise false positives.

Regarding the first point, I was planning to do combinations of pairwise comparisons to generate DE within the 3 reps (using edgeR or DESeq) but I'm unsure how to then use this to refine the pooled data DE Ė any ideas or any references where this has been done already? (Or (a) am I totally on the wrong track, (b) is it blindingly simpleÖ?)

Any advice would be greatly appreciated, thanks in advance!
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