Normalized expression

[livnatje]

Hi,

Thanks again for making this great and very useful algorithm accessible :).

I have a question concerning the output of the pagoda.varnorm function. The "mat" output is the normalized dataset, correct? Some genes get a zero value across all cells, even though they are (1) adequately expressed, and (2) scde quantifies their differential expression between groups.

Why doesn't pagoda.varnorm generate their normalized expression then?
Would be great to get some clarification.

Thanks a lot,
Livnat