Question: read.FCS memory limit? - $PnRNAis larger than R's numeric limit
gravatar for lloyd.izard
10 weeks ago by
lloyd.izard30 wrote:

Good morning,

I am trying to read from a FCS file but I get the following error:

Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale,  : 
  $PnRNAis larger than R's numeric limit:1.79769313486232e+308
In addition: Warning message:
In readFCSdata(con, offsets, txt, transformation, which.lines, scale,  :
  NAs introduced by coercion

The thing is, when I try to read the same file in .csv format, I can read it!

# library


# data

data <- read.table('file.csv', dec = ".", sep = ",")
data <- read.FCS('file.fcs', alter.names = F, transformation = "linearize")

My question is: is there a memory limit for read.FCS()? And if so, how do I extend it?

All the best, Lloyd Izard

ADD COMMENTlink written 10 weeks ago by lloyd.izard30


I don't suspect a memory limit there. The read.FCS has been extended recently to cope with file bigger than 2GB. The error sounds like a problem in reading and interpreting the TEXT segment of the FCS file. Of course reading a CSV file avoids this problem because there is no such meta data. I think you should report the error onto You should report the sessionInfo() result and share some information about the FCS: instrument...

Meanwhile, you could verify that the FCS complies with FCS standard using flowIO (CLIP, Prague) or (Zach Bjornson).


ADD REPLYlink modified 9 weeks ago • written 10 weeks ago by SamGG180
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 319 users visited in the last hour