multi sample/batch data

[gianfilippo]

Hi,

what is the best way to run SE_fun in the case of multiple samples/batches ?
do I run it on each sample, i.e. select genes with p.adj<0.05 (or similar) for each sample, than combine them all together or should I run it on then combined count matrix of all samples, i.e. assuming SE_fun is not affected by batch ?

Thanks