Error running BuildSOM on FlowCAP data

[jess310t]

Hi, Thanks for sharing the code first.
I was running into the same issue, with the flowCAP ND data -- I didn't try the other datasets.

I also looked into the vignette and tried to use their example code with the package included sample datasets.
Their sample code and sample datasets worked all just fine without error.

Here's the sample code I used:

fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
ff <- flowCore::read.FCS(fileName)
flowSOM.res <- FlowSOM::ReadInput(ff,scale=FALSE, transform=FALSE)
flowSOM.res <- FlowSOM::BuildSOM(flowSOM.res,colsToUse=c(9,12,14:18))

I compared the flowSOM object after ReadInput and there was no obvious difference between loading your datasets and the sample datasets. I wonder if you have any insights on what the problem may be?

The error that I received is:

Error in if (length(y) > 0 && mean(y) != 0) {: missing value where TRUE/FALSE needed
Traceback:

1. system.time({
 .     fSOM <- FlowSOM::ReadInput(data[[j]], transform = FALSE, 
 .         scale = FALSE)
 .     fSOM <- FlowSOM::BuildSOM(fSOM, colsToUse = c(3:12), xdim = grid_size, 
 .         ydim = grid_size)
 .     fSOM <- FlowSOM::BuildMST(fSOM)
 . })
2. FlowSOM::BuildSOM(fSOM, colsToUse = c(3:12), xdim = grid_size, 
 .     ydim = grid_size)
3. UpdateDerivedValues(fsom)
4. t(sapply(seq_len(fsom$map$nNodes), function(i) {
 .     apply(subset(fsom$data, fsom$map$mapping[, 1] == i), 2, function(y) {
 .         if (length(y) > 0 && mean(y) != 0) {
 .             stats::sd(y)/mean(y)
 .         }
 .         else {
 .             NA
 .         }
 .     })
 . }))
5. sapply(seq_len(fsom$map$nNodes), function(i) {
 .     apply(subset(fsom$data, fsom$map$mapping[, 1] == i), 2, function(y) {
 .         if (length(y) > 0 && mean(y) != 0) {
 .             stats::sd(y)/mean(y)
 .         }
 .         else {
 .             NA
 .         }
 .     })
 . })
6. lapply(X = X, FUN = FUN, ...)
7. FUN(X[[i]], ...)
8. apply(subset(fsom$data, fsom$map$mapping[, 1] == i), 2, function(y) {
 .     if (length(y) > 0 && mean(y) != 0) {
 .         stats::sd(y)/mean(y)
 .     }
 .     else {
 .         NA
 .     }
 . })
9. FUN(newX[, i], ...)

[jess310t]

To be more exact I was using the dataset FlowCAP_ND.fcs from https://flowrepository.org/id/FR-FCM-ZZPH.