regressing out confounders for differential expression

[livnatje]

Hi,

I've tried regressing out (continuous) confounders (e.g., cell cycle) so that the differential expression results won't be effected by them, but it doesn't work. I get the same results. I tried using pagoda.subtract.aspect, but then when I run scde.expression.difference, it makes no difference.

Would be great if there is a way to make it work.

Thanks a lot!
Livnat