Closed rprops closed 5 years ago
experiencing similar errors with diversity_rf
does this occur on flowAI denoised data or on normal data too?
in my case it occured on normal (i.e. transformed, but not cleaned) data too, I looked at Diversity_rf
and it happens when applying x <- x[, param]
. R version 3.5.3 (2019-03-11), on linux, Phenoflow installed from GitHub 8d58f48
specifically, this type of subsetting appears to break after running mytrans
in flowCore::transform
I have pinpointed the issue (at least in my dataset). Right before the mytrans
normalization, we use flowCore::Subset
to separate the cellular fraction. It would appear that, at least in my case, some samples retained 0 cells. This makes the transformation return a non-numeric matrix (i.e. a null matrix), which returns the error. Diagnostic: which(unlist(fsApply(flowData_transformed,function(x)is.numeric(x@exprs)))==FALSE)
if this returns anything else but named integer (0)
there are samples that are problematic. Even with 1 cell, it will still work, therefore I am now applying an additional subsetting step to assure that there are at least 500 cells in the sample.