Hello,

In DEG analysis using edgeR or limma, is there a requirement on the minimum number of samples to compare? Can I just compare 1 treatment against 1 control, each with multiple replicates?

Regards

There is no requirement for a minimum number of samples, apart from the requirement that there must be some replication. Since there must be at least two different experimental conditions in order to have something to compare, and there must be more samples than groups in order to have any replication, it follows that the absolute minimum number of biological samples is 3. An example of an absolute minimal experiment would be to compare n=2 treatment samples to n=1 control sample, something that is perfectly possible in edgeR although not something we would recommend as good experimental practice.

If you have multiple replicates for both treatment and control, then you seem set to go.