Reading fcs files generated through PeacoQC by Cytonorm

[Shuaiwei-Wang]

Hi there,

After running PeacoQC, I got errors for training the the generated train files when using Cytonorm. I had no problem for training and normalizing the original fcs files. I am wondering if Cytonorm is suitable for normalizing the PeacoQC-corrected fcs files. It will be much appreciated if you have any clues.

The errors I got:
Splitting /Users/wswimmune/Documents/Work/Postdoc/Experiments/CRUSTY/CD56dimCD16poNK/PeacoQCresults/PeacoQC_results/fcs_files/Con018_1_QC_1.fcs
Error in newdata[, colnames(codes)] : subscript out of bounds
In addition: Warning message:
In CytoNorm.train(files = train_data$Path, labels = train_data$Batch, :
Reusing FlowSOM result previously saved at ./tmp/CytoNorm_FlowSOM.RDS

traceback()
3: MapDataToCodes(fsom$map$codes, fsom_new$data)
2: FlowSOM::NewData(fsom, ff)
1: CytoNorm.train(files = train_data$Path, labels = train_data$Batch,
channels = markerstotransform, transformList = NULL, truncate_max_range = FALSE,
FlowSOM.params = list(nCells = 6000, xdim = 5, ydim = 5,
nClus = 10, scale = FALSE), normMethod.train = QuantileNorm.train,
normParams = list(nQ = 101, goal = "mean"), seed = 1, verbose = TRUE)

Best wishes