questions about differentially expressed genes analysis

[Roger Z]

Hello! I an preparing the samples and designing the analysis scheme for RNA-seq. I want to use two groups of samples to do differential analysis, do all the samples in a group need to be biological replicates? Can it be technical replicates?

[jwfoley]

Of course you need biological replicates! What you're going to be testing, for each gene, is whether the difference between groups is greater than the difference within groups. You can't do that if you don't know the differences within the groups. See doi:10.1093/bioinformatics/btt688 for some numbers.

Technical replicates were standard with microarrays because of the technical noise, but that's not really an issue for RNA-seq so they're not usually done.

[Roger Z]

Hi, Jwfoley, thanks a lot.