edgeR for unequal replicated samples

[hchang10]

Hi folks,

I have a question about how to do DE analysis of an unequal replicated RNA-Seq data? The design looks like:

Treatment 5day 7day 9day
A 1rep 3reps 1rep
B 1rep 3reps 1rep

The interest is to see the difference between treatments and over time.

Can edgeR handle that? Or any other recommended programs?

I appreciate a lot!

[Gordon Smyth]

If I understand you correctly, you have multiple replicates at 7 days but not at 5 days or 9 days.

edgeR handles that automatically. All it requires are replicates for at least one condition. There is no requirement for equal numbers of replicates at each time or treatment.