Hi Biostars,

Is it legitimate to sum up raw read counts from technical replicates of RNAseq, and use these summed counts for DE analysis. Would appreciate detailed and justified answers. 

Thanks
There is a theoretical justification for summing and not averaging. Read counts follow a Poisson distribution so averaging them results in data that is not Poisson, but summing is still Poisson. See Mike Love's explanation [here][1] 


  [1]: http://seqanswers.com/forums/showthread.php?t=60996#4