Question

Cannot open Sysmex Partec CUbe 6 .fcs with read.FCS

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Entering edit mode

mrescan • 0

@c49e2e69

Last seen 12 months ago

Spain

Hello,

I am trying to read .fcs from a Sysmex Partec Cube 6 V2M flow cytometer, and get an error (with (R 4.2.1, flowCore2.10.0):

> library(flowCore)
> isFCSfile("AEboth")
AEboth 
  TRUE 
> read.FCS("AEboth")
Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale,  : 
  object 'dat' not found

I am not expert enough to dig in the function code, and I do not see what is wrong with the .fcs. I can read it with other interfaces.

Thank you for your help,

Best,

Marie

Partec read.FCS flowCore • 642 views

ADD COMMENT • link 12 months ago mrescan • 0

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Hi,

I don't know whether traceback() would give more details. I went through read.FCS code, but didn't get any clue.

If you could share the file, it would be easier. My mail is on github if you need a private share.

I think this issue would deserve opening an issue on github https://github.com/RGLab/flowCore/issues

Best.

ADD REPLY • link 12 months ago SamGG ▴ 350

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Entering edit mode

Thanks a lot for this quick answer.

traceback() returned:

2: readFCSdata(con, offsets, txt, transformation, which.lines, scale, 
   alter.names, decades, min.limit, truncate_max_range, channel_alias)
1: read.FCS("AEboth")

I installed the package IFC to get get the function readFCSdata(), could not find it, but tried readFCS(), which works (problem solved for me) but with a warning:

Warning: TEXT (or sup. TEXT) segment: can't find final delimiter Warning: TEXT (or sup. TEXT) segment: can't find final delimiter Warning: TEXT (or sup. TEXT) segment: supplemental TEXT segment is not readable: embedded nul in string: 'P [... truncated]

I will submit this issue to the github, thanks for the suggestion

Best,

Marie

AEboth.fcs (FCS3.0) file

ADD REPLY • link 12 months ago mrescan • 0