Entering edit mode
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