rpalaganas
rpalaganas
I did not filter genes with zero expression
Good morning, Sorry for the delay. After removing zero variance and zero expression genes with ``` #drop zero expression genes row_sums
The sparsity of the matrix that gave the -nans is 0.71. `coop::sparsity(Hoxd10) #0.7125972` I also do not get -nan ChiSq when testing a matrix that is almost exactly as sparse....
> Is this data more than 80% sparse? Slightly less, ~71% sparse
sure, see below ``` #sparse optimized and not distributed devtools::install_github("FertigLab/CoGAPS@77-sparseoptimization-pattern-discrepancy") library(CoGAPS) params
I don't see any issues