How to fix fix $PnR in flowCore
0
0
Entering edit mode
Elle • 0
@579e5dad
Last seen 4 months 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 • 297 views
ADD COMMENT

Login before adding your answer.

Traffic: 1113 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6