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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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regressing out confounders for differential expression #68

Open livnatje opened 6 years ago

livnatje commented 6 years ago

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