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Compensated files in Cytobank

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SaraAli

Participant

Posts: 10

Joined: Wed Jan 10, 2018 3:37 pm

Post Sun Sep 30, 2018 4:47 pm

Compensated files in Cytobank

Hi,

I'm trying to run ViSNE on some files that I normalized (using the MATLAB method), concatenated and compensated using the CATALYST package but I'm getting this warning message after uploading it onto Cytobank: "This file contains overlapping segments. The Text Segment ends at byte 10560 and the Data Segment starts at byte 7728. This is an overlap of 2833 bytes."

Any idea what could be the problem?


Many thanks!
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Sun Sep 30, 2018 7:24 pm

Re: Compensated files in Cytobank

Hi,
It sounds like https://github.com/HelenaLC/CATALYST/issues/41
Check the version of flowCore
packageVersion("flowCore")
and may be update it
https://github.com/RGLab/flowCore
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SaraAli

Participant

Posts: 10

Joined: Wed Jan 10, 2018 3:37 pm

Post Tue Oct 16, 2018 4:03 pm

Re: Compensated files in Cytobank

Thanks for your reply.
I had a similar problem to the one mentioned in the link you provided but that was to do with the way I was writing the FCS file. Changing endian from big to little solved the problem. However, I still could not read the compensated file in Cytobank despite it working in Flowjo. After many attempts of trying to solve this, I loaded the compensated file into Flowjo and exported it again and it is working now on Cytobank!
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Tue Oct 16, 2018 8:48 pm

Re: Compensated files in Cytobank

Many thanks for sharing the solution.

I have just checked the endian point: I loaded a big endian FCS 2.0 and wrote it without mentioning the endian parameter. The resulting file is in little endian format. I guess we don't have the same flowCore version. Mine is :
  Code:
> packageVersion("flowCore")
[1] ‘1.47.8’

Best.

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