Hello,

I am a graduate student and fairly new to RNA-Seq. In my study I have a 2x2
design with each group containing 4 bio reps and each bio rep has 3
technical replicates (same library prep, but each sample is processed in 3
different lanes). After studying my frequency count data I have found that
the count data in lane 1 is very different from lane 2 and 3 for most to
all bio samples. I plan to use EdgeR for DE analysis and I am wondering if
it is OK to sum count totals from just lanes 2 and 3. All documentation I
have read states that technical variation is small so you should sum all
tech reps, but in this case it seems I have noticed greater variation in
one lane and therefore it does not make sense to include it. I have not
found any reason why you can not just sum 2 out of 3 technical replicates
if you know that one technical replicate has much higher variation than the
other two. Please let me know if you have any evidence for this.

Thank you very much in advance.

-- 

Neha Mehta
---------------------------------------
PhD Candidate, Neuroscience
Northwestern University
ph. (412) 874-6342
e. nsmehta@u.northwestern.edu

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