CytoNorm.normalize() creating unknown .fcs files

[emilier17]

Hello,

I'm experiencing an issue when using CytoNorm.normalize(). The function properly generates the new normalized fcs files, and they are placed in the folder I specify in outputDir. However, there are also a bunch of other .fcs files created whose filenames appear to be the filepaths to the input data.

Here is how I used the function:

CytoNorm.normalize(model = norm_model,
files = sample_files,
labels = sample_labels,
transformList = NULL,
transformList.reverse = NULL,
normMethod.normalize = QuantileNorm.normalize,
outputDir = file.path(results.dir, "normalization/FCS_norm"),
prefix = "Norm_",
clean = TRUE,
verbose = TRUE)

Here is an example of the files I find in the specified outputDir:

Correctly named sample example (there are 8 files, as expected):
Norm_BAS_SUR_AA22008_2022-03-14_Peanut1_QC.fcs

Unknown files example names (there are 100 of these files):
C__Users_emili_Desktop_emilier_flowSOM_results_QC_PeacoQC_results_fcs_files_BAS_SUR_AA23013_2024-07-31_Peanut_QC.fcs_fsom1.fcs

What is the potential cause for these unknown files to be created and not removed ? What should I change to the script to fix this issue?

Thank you!