use prenormalized matrix for cNMF about cnmf HOT 1 CLOSED

Hi @sumitava1992 - sorry for the slow reply. Do you want to use all of the genes in the prenormalized matrix? If not, you should indicate that you want to use all of the genes in the --num_genes argument. And are you okay with the fact that cNMF will variance normalize the genes (in addition to whatever normalization you did)? I haven't implemented an argument to tell it not to do that currently. And then lastly the question is what scaling you want the data to be in when it refits the spectra. I think you likely would still want to submit a normalized tpm or tp10k matrix for the --tpm argument, and your prenormalized matrix to the -c argument. Hope that helps!

from cnmf.