search

cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
56 stars 14 forks source link

Question about differentialGeneTest #9

Closed danielee0707 closed 5 years ago

danielee0707 commented 5 years ago

I noticed that some of the examples in Cicero tutorial use num_genes_expressed in full model while others (also in Monocle tutorial) don't. What's the reason for that and when should we use it? Thanks!

hpliner commented 5 years ago

Adding the num_genes_expressed to the full model is a way of being extra conservative with ATAC data in making sure reads per cell/depth is accounted for. Strictly speaking it shouldn't generally be necessary since the calculation already takes Size_Factor into account. Hope this helps!