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Cytofkit

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Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
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ErinSimonds

Master

Posts: 50

Joined: Tue May 13, 2014 8:04 pm

Post Wed Feb 07, 2018 8:28 am

Re: Cytofkit

Shiny is a way for R to load up a webpage-like GUI in your web browser. It sounds like it is starting the Shiny server correctly, but not opening your browser to the URL automatically. Try opening a modern browser (Chrome/Firefox) and pointing it to http://127.0.0.1:4455 shortly after you get past the prompt to run Shiny, and while R is still runnning.
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nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Wed Feb 07, 2018 8:37 am

Re: Cytofkit

Thanks for the quick replies, Erin and Samuel. Its working now.
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nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Wed May 02, 2018 10:51 am

Re: Cytofkit

I have recently updated my R to version 3.5.0 and find that cytofkit doesn't work. Has anyone else had this problem?
Naeem
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Wed May 02, 2018 12:03 pm

Re: Cytofkit

Hi,
No answer, but I think:
a) you should precise the error by posting the error message and the session info
b) you should open a new issue @ github
Meanwhile, I think you could easily downgrade to R 3.4.4 unless you remove it with all its libraries.
Best.
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rosskedl

Participant

Posts: 1

Joined: Tue Jun 26, 2018 7:08 pm

Post Tue Jun 26, 2018 7:34 pm

Re: Cytofkit

I am having the exact same issue as a previous user for whom the advice was to install the command line tools... which i have and have updated. my error message is the same as theirs...

> library("cytofkit")
Error: package or namespace load failed for ‘cytofkit’:
.onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libfontconfig.1.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: Incompatible library version: libtk8.6.dylib requires version 11.0.0 or later, but libfontconfig.1.dylib provides version 10.0.0
> cytofkit_GUI()
Error in cytofkit_GUI() : could not find function "cytofkit_GUI"

does anyone know a fix for this? is there a way to update the library?
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Oshbosh

Participant

Posts: 4

Joined: Wed Feb 24, 2016 1:56 pm

Post Mon Aug 13, 2018 10:31 am

Re: Cytofkit- Problem with fcs export

Hi all,
I'm having a problem with the exported fcs files after a CyTOFkit analysis. In the shinyapp visualisation it looks great (left) but the fcs files don't contain the tSNE coordinates and the files look really strange (right). See attached picture. Has anyone else had similar problems?
Cheers
Osh
Attachments
CyTOFkit trouble.png
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Mon Aug 13, 2018 10:51 am

Re: Cytofkit

Hi,
Others are also reporting reporting recent similar issues
https://github.com/JinmiaoChenLab/cytofkit/issues
https://github.com/JinmiaoChenLab/cytofkit/issues/41
I think the developer is trying trying to solve them.
Best.
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taxkourel

Participant

Posts: 14

Joined: Sun Sep 03, 2017 3:46 pm

Post Tue Aug 14, 2018 8:25 pm

Re: Cytofkit

I get the following error message when trying to run a cytofkit analysis:

"Extract expression data...
Error in fcsTextParse(txt, emptyValue = emptyValue) :
Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!"

If I run the same analysis in the raw or normalized files it runs ok.

This is my workflow
1) Normalize raw files
2) Correct channels using premessa since during acquisition some channels had different names and need them to match across all files
3) Upload to cytobank for live/dead gating. I also "gate out" some populations I dont plan to use at all for downstream analyses. This creates a few daughter populations of interest that I need to merge
4) I then concatenate (cytobank tool) these daughter populations of interest and plan to use that as my clean population for analyses.

I have no issues using the concatenated files in cytobank. Only in cytofkit I get this issue.

Any idea what went wrong and what I can do to fix it?
Could it be that premessa is messing up things and confusing it?
Any way to fix this using my existing files so I dont have to start all over again?

Thank you for your help!
Tax
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taxkourel

Participant

Posts: 14

Joined: Sun Sep 03, 2017 3:46 pm

Post Tue Aug 14, 2018 9:01 pm

Re: Cytofkit

taxkourel wrote:I get the following error message when trying to run a cytofkit analysis:

"Extract expression data...
Error in fcsTextParse(txt, emptyValue = emptyValue) :
Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!"

If I run the same analysis in the raw or normalized files it runs ok.

This is my workflow
1) Normalize raw files
2) Correct channels using premessa since during acquisition some channels had different names and need them to match across all files
3) Upload to cytobank for live/dead gating. I also "gate out" some populations I dont plan to use at all for downstream analyses. This creates a few daughter populations of interest that I need to merge
4) I then concatenate (cytobank tool) these daughter populations of interest and plan to use that as my clean population for analyses.

I have no issues using the concatenated files in cytobank. Only in cytofkit I get this issue.

Any idea what went wrong and what I can do to fix it?
Could it be that premessa is messing up things and confusing it?
Any way to fix this using my existing files so I dont have to start all over again?

Thank you for your help!
Tax


I do note that this is only an issue when I include concatenated files after step 4.
Basically I am gating out malignant cells, but some of them are "hidden " in the CD45+ compartment that is why I need to create some 2D gates to exclude them. I then export these clean CD45+ populations (max of 3 separate population/sample) and merge them to a new fcs file. I note that the "merged" files are causing the problem. If I use e.g. healthy donor samples I have no problems (no malignant cells, just one population is exported and thus no need for concatenation-). My guess is that cytofkit reads these 2 differently somehow but not sure what to do.

Any thoughts are greatly appreciated. :-(
Tax
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conorisco

Participant

Posts: 2

Joined: Tue Sep 04, 2018 4:40 pm

Post Tue Sep 04, 2018 4:55 pm

Re: Cytofkit

Hi Guys,

Also getting the same problem when I run CytofKit. Everything looks great but the exported FCS files are unreadable, exactly the same as the previous user has reported.

I could try downgrading R. to see if that is the issue.

Only problem is I have done probably weeks of analysis, and since the FCS files are useless, I'll probably have to dump it.

Anyone hear of a fix for this?

Cheers
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