Error in quantile.default(x, seq(from = 0, to = 1, length = n)) :

[naity]

The following error was encountered while running DSBNormalizeProtein:

Error in quantile.default(x, seq(from = 0, to = 1, length = n)) :
missing values and NaN's not allowed if 'na.rm' is FALSE

Thank you!

[MattPM]

Hi, @naity, it is tough to know where the error might be coming from without a reprex, knowing what you have already tried to troubleshoot the issue and the function call that produced the error. Do you have a traceback() or a sessionInfo() call? Are there NA's in the matrix you're using? Maybe remove those first, but without more info not sure exactly where to start. Happy to help though.

[MattPM]

update: @naity this error occurs during denoising, when you have antibodies in the cells (not the empty drops) that have close to zero counts across all cells. I am assuming you used denoise.counts = TRUE Please try checking the distributions of your staining antibodies - for example run apply(cells_protein_matrix, 1, quantile) or apply(cells_protein_matrix, 1, mean) and check if you have a protein with basically no counts, try removing it and renormalizing(recommended) or set denoise.counts = FALSE

[naity]

Thank you for the explanation!