Hello

I am using SomaticSignatures package for data analysis. If I have four cancers under study should the number of samples for each cancer type be the same. I mean to ask that is this alright if for one cancer type I have data for 200 samples and for other cancer type I have data for 400 samples. Would the analysis by SomaticSignatures be reliable in such case?

Can someone kindly answer my question?

Regards 

The number of samples in each group can differ, i.e. your design of 200 vs 400 samples does not pose a problem. To account for different numbers of mutations, the motif matrix gets normalised and does not use the absolute number of variants. You can have a look at the vignette to see an example of this.