This is the error I am getting:
> scfp3 <- SCTransform(scfp3, method = "glmGamPoi", vars.to.regress = "percent.mt", verbose = FALSE) Error in density.default(x = genes_log_gmean_step1, bw = "nrd", adjust = 1) : 'x' contains missing values In addition: Warning message: In vst(method = "glmGamPoi", umi = new("dgCMatrix", i = c(0L, 2L, : NaNs produced
I think this error might be because there are zero integers in the expression matrix. For example the data frame looks like this
Could someone help me solve this, please? I have been messing around with changing Na to zeros and vice versa, no solution yet. I will keep trying.