unbalanced number of replicates

[LandiMi2]

Hello, I do have an unbalanced number of replicates for my conditions. Can I read these unbalanced numbers of replicates as one, say, one condition A has 5 replicates and the other B has 3 replicates? Use these conditions A and B as pooled data, so I run the analysis as A and B to compare methylation between these groups. will DSS handle this kind of bias?

[joao-chrusciel]

I've got the same situation. Did you manage to figure it out?

[haowulab]

This is not a problem. DSS will handle that.