mm_glmm("nbinom") returns NAs

[Nayrouz109]

Hello,

I have 2 quick questions and would appreciate your help!

Q1: I have tried running mmDS( sce, method = "nbinom") on one cluster to test it out and it returned a table of "NA"s. I was wondering if you have any idea what might have gone wrong.

Q2: I want to clarify whether your normalized counts after or before you aggregate data in the paper. When you ran limma-voom.sum did you sum the counts of raw data -> aggregate -> DE analysis ? and when you ran limma-trend.mean did you take the mean of logcounts -> aggregate -> DE analysis ?

Thank you,