Zhentao Liu

> Hi, > > DE analysis is performed on all of the genes included in the input (not just the highly variable genes used for iNMF). > > Best, Thanks...

> It seems that in your case, DE analysis would be a problem if you try to find DE genes between different batch datasets because of the batch effects. However,...

> The way we do DE gene analysis is (1) find joint clusters using LIGER and (2) perform Wilcoxon rank-sum test between datasets within each joint cluster. This relies on...