error in bcRegressout

[Lukadon77]

when I regressout the bc S4 object
bcRegressOut(bc, add.DSS = T,
vars.to.regress = c("nFeature_RNA"))
it stops with the following error:
#Error in rep(1, ncol(dist)) : nvalid 'times' argument.
How can I fix this bug?

[Jojojo-1990]

I met the same question!!! Do you figure out how to fix it? I actually don't really know what steps should be done to get the correct rds file as the input for beyondcell.

[SGMartin]

@Lukadon77 @Jojojo-1990

Hey, sorry for the late reply

Unfortunately, this is a common issue caused by the imputation step of the regression. At the moment, we suggest just replacing the NaN values with 0s. See the following code snippet:

 # Do not allow NaNs
    bc@normalized[is.na(bc@normalized)] <- 0
    bc <- bcRecompute(bc, slot = "normalized")
    bc <- bcRegressOut(bc = bc, vars.to.regress = c("nFeature_RNA"))