Hello,

I have a small query with respect to running eisaR. I have three replicates each for control and treatment samples. I am able to generate the individual alignment files (bam files), followed by the generation of the count table. I would like to know how to indicate the files as replicates, for the program to perform statistical analysis between the replicates of control and experimental samples.

Thank you

Regards Nishanth

That is done via the cond argument to runEISA(), where you specify the group that each sample belongs to (control or treatment) - see section 5 in the vignette.