FlowSOM fails after CytoNorm

[vivek-verma202]

Hi Sofie,
Thank-you for FlowSOM!
I was able to successfully run FlowSOM on the raw data but failed when the fcs files were normalized using CytoNorm. I believe, this error is because of introductions of NAs. How can I debug / circumvent this?

     sce <- cluster(sce, features = "type",
     +                xdim = 10, ydim = 10, maxK = 10,
     +                verbose = T, seed = 1)
     > o running FlowSOM clustering...
     > Error in SOM(fsom$data[, colsToUse], silent = silent, ...) : 
     > NA/NaN/Inf in foreign function call (arg 1)

By default,

     > options("na.action")
     $na.action
     [1] "na.omit"

am using R v4.0.0
and FlowSOM v1.20.0

Thanks a lot!
Vivek

[vivek-verma202]

The issue was:

> sum( is.infinite(assay(sce, "exprs")) )
[1] 79
> mean( colSums( is.infinite(assay(sce, "exprs")) ) > 0)
[1] 5.214521e-06

It was fixed by:

sce <- filterSCE(sce, colSums(is.infinite(assay(sce, "exprs"))) == 0)

Detailed troubleshooting is here