Warning: Some data values of ... channel exceed its $PnR value 175864747 and will be truncated! To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'?

[denvercal1234GitHub]

Hi there,

Thank you for the package.

Following up on #109, I too encountered a warning/advice to "avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'" during write.FCS when performing the infinity_flow() (ebecht/infinityFlow#20)

Reading https://support.bioconductor.org/p/130629/, it looks like the solution is to perform range(fr, type = "data") after read.FCS() to use the min/max taken from the actual data so that when export, write.FCS will not use the default instrument values.

@SamGG seemed to hint at https://github.com/ParkerICI/premessa to append truncate_max_range = FALSE in #169

Is performing range what people typically do and all I should do?

Thank you again very much for your help.

fr <- read.FCS(fcs_file_path)
range(fr) # will default to instrument range
range(fr, type = "data") # Will use the actual values, as in summary

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] infinityFlow_1.6.0 flowCore_2.10.0   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10         lattice_0.20-45     codetools_0.2-19    matrixStats_0.63.0  RProtoBufLib_2.10.0
 [6] png_0.1-8           grid_4.2.2          stats4_4.2.2        pbapply_1.7-0       sp_1.6-0           
[11] raster_3.6-20       S4Vectors_0.36.1    generics_0.1.3      tools_4.2.2         Biobase_2.58.0     
[16] parallel_4.2.2      compiler_4.2.2      terra_1.7-18        BiocGenerics_0.44.0 cytolib_2.10.1     
[21] matlab_1.0.4    

[mikejiang]

range(fr, type = "data") is read-only accessor which doesn't mutate your data, besides once your data is read through fr <- read.FCS(fcs_file_path), data is potentially already truncated, there will be no point to further correct range information.
I think you just need to switch truncation off when you read the file
fr <- read.FCS(fcs_file_path,truncate_max_range=F)

[denvercal1234GitHub]

Thank you @mikejiang.

In our case, unfortunately, having read.FCS(truncate_max_range=F) does not seem to solve the issue because I still got the warning when I ran the infinity_flow() function from infinityFlow package (ebecht/infinityFlow#20).

Looking into the codes of infinity_flow() at line 16 (https://github.com/ebecht/infinityFlow/blob/master/R/00_master.R), it appears that truncate_max_range was already set to FALSE.

#' @param extra_args_read_FCS list of named arguments to pass to flowCore:read.FCS. Defaults to list(emptyValue=FALSE,truncate_max_range=FALSE,ignore.text.offset=TRUE) which in our experience avoided issues with data loading. 

[gfinak]

So what problem are you actually having and what makes you believe it's a flowcore issue? Do you have some code we can use to reproduce the issue to work off of?