read.flowSet error Error: vector::_M_range_check
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Entering edit mode
e.bestion • 0
@ebestion-9746
Last seen 5.8 years ago

Hi,

I am encountering an error when trying to run the read.flowSet. I have a folder of .fcs files from a 96 well plate, one file per well. I concatenate the info into a dataset, but recently I have started to have errors when running my code, which is due to the read.flowSet command returning Error: vector::_M_range_check.

The only option I found is to delete the fcs file corresponding to the faulty well, and run my loop again, but it is particularly cumbersone and I am loosing a lot of data doing so.

It is noteworthy that the read.FCS command also returns this error message.

fnames <- list.files(pattern=".fcs") # find all FCS files
dataset<-data.frame() #create empty data frame
loc0events<-vector() #create vector


for (i in 1:length(fnames))      #loop through all files
{
  data<-read.flowSet(fnames[i])  # tell R that all files are flowfiles
  data<- data.frame(cbind(exprs(data[[1,7]]),exprs(data[[1,8]]),exprs(data[[1,11]]),exprs(data[[1,10]]),exprs(data[[1,12]]),exprs(data[[1,9]]))) #extract data from flow files

  # add column for volume in µl
  dataverif <- read.FCS(fnames[i]) ;
  vol=round((as.numeric(dataverif@description[['$VOL']])/1000),0)
 
  #add identifier column
  plateloc<-gsub(".fcs","",fnames[i])
 
  if(dim(data)[1]!=0) # for wells where there are events
  {
    data<-cbind(plateloc, data)       # add new column to existing dataset
    volumesampled<-rep(vol,dim(data)[1])
    data<-cbind(data,volumesampled)
    dataset<-rbind(dataset, data)  #combine all rows to a big file  
  }
  else #for wells where there are no events
  {
    loc0events<-c(loc0events,plateloc)
  }
}

Error: vector::_M_range_check

#if  Error: vector::_M_range_check -> remove info in the folder
levels(dataset$plateloc)

 "A01" "A03" "A04" "A05" "A08" "A09" "A10" "A11" "A12" "B01" "B05"

here I should remove the B05.fcs file

 

 

software error read.flowset() read.fcs flowcore flowcytometry • 880 views
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Entering edit mode

Can you send me B05.fcs for troubleshooting?

BTW, your first 3 lines can be simplified by 

 fr <- read.FCS(fnames[i])  # tell R that all files are flowfiles
  data<- data.frame(exprs(fr)[, c(7:12)]) #extract data from flow files
  
  # add column for volume in µl
  dataverif <- fr
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