How to fix fix $PnR in flowCore
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Elle • 0
@579e5dad
Last seen 3 days ago
United Kingdom

I'm facing a problem with flowCore Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29)

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("flowCore")

library('flowCore')

sessionInfo( Warning message:
package(s) not installed when version(s) same as or greater than
  current; use `force = TRUE` to re-install: 'flowCore'  )

so I entered

BiocManager::install("flowCore", force = TRUE)


sessionInfo( Old packages: 'Hmisc', 'knitr', 'SparseM'
Update all/some/none? [a/s/n]: )

then I entered a and was downloaded

However when r read FCS file received a warning as below

> x<- read.FCS("~/Downloads/Specimen_001_Tube_001.fcs", transformation = FALSE)

Warning messages:
1: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of 'FSC-A' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
2: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of 'FSC-W' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
3: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of 'SSC-A' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
4: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of 'SSC-W' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
5: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of '488 530/30-A' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
6: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of '488 530/30-H' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
7: In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  Some data values of '488 530/30-W' channel exceed its $PnR value 262144 and will be truncated!
 To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'

I tried

> x<- read.FCS("~/Downloads/Specimen_001_Tube_001.fcs", transformation = FALSE, truncate_max_range = FALSE)

but still facing the same warning

flowCore • 96 views
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