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Old 08-22-2014, 12:27 PM   #1
hchang10
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Location: UIUC

Join Date: May 2013
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Default edgeR for unequal replicated samples

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!

Last edited by hchang10; 08-22-2014 at 12:30 PM.
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Old 08-27-2014, 11:32 PM   #2
Gordon Smyth
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Default

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.
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