Question

FlowSOM BuildSOM Error

1

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katharina.kriegsmann ▴ 10

@katharinakriegsmann-23688

Last seen 5.5 years ago

Hi, I was wondering whether anybody could help with the following problem that occurs when using FlowSOM in the context of this code: https://github.com/sydneycytometry/CAPX.

> ## run FlowSOM (initial steps prior to meta-clustering)
>   FlowSOM_out <- FlowSOM::ReadInput(data_FlowSOM, transform = FALSE, scale = FALSE)
> FlowSOM_out <- FlowSOM::BuildSOM(FlowSOM_out, colsToUse = FlowSOM_cols)
Building SOM
Mapping data to SOM
Error in if (length(y) > 0 && mean(y) != 0) { : 
  missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
>

Katharina

FlowSOM::BuildSOM • 1.0k views

ADD COMMENT • link updated 4.6 years ago by Jessie • 0 • written 5.5 years ago by katharina.kriegsmann ▴ 10

0

Entering edit mode

I wonder if anyone else is facing a similar problem. I too got the error when ReadInput from a flowFrame, then BuildSOM.

fSOM <- FlowSOM::ReadInput(data[[j]], transform=FALSE, scale=FALSE)
fSOM <- FlowSOM::BuildSOM(fSOM,colsToUse =c(3:12),
                                 xdim = grid_size, ydim=grid_size)

class(data[[j]]) is 'flowFrame', with a summary :

flowFrame object 'FlowCAP_ND.fcs'

with 60418 cells and 14 observables:
            name desc range   minRange     maxRange
$P1 FSC-A NA 1024 0.0000000 2.621430e+05 ...

which is processed from the FlowCAP dataset

I received the same error:

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

ADD REPLY • link 4.6 years ago Jessie • 0