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ParkerICI / premessa

R package for pre-processing of mass and flow cytometry data
GNU General Public License v3.0
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error while debarcoding #13

Closed nsigal closed 6 years ago

nsigal commented 6 years ago

I suddenly started getting error during debarcoding. I can loads the CSV and the FCS and see the plots but it crashes during the attempt to save the daughter files.

screen shot 2018-05-07 at 10 17 11 am

R, Rstudio and all relevant packages are updated. Any ideas? Thanks! Natalia

pfgherardini commented 6 years ago

Hi Natalia,

Can you please share with me the data you are trying to debarcode so that I can reproduce and fix the issue on my system?

Thanks

Federico

nsigal commented 6 years ago

yes, definitely. Here are fcs file and the key code: https://drive.google.com/drive/folders/1xbDHLvl4nlJUjxj2lWr6aQ_9VTnGJrYK?usp=sharing BTW I learned today that I if I change the setting from separation 0.3 to 0.1 and MD from 30 to something like 5, I am able to save the data.

Natalia

From: Pier Federico Gherardini notifications@github.com Reply-To: ParkerICI/premessa reply@reply.github.com Date: Monday, May 7, 2018 at 3:50 PM To: ParkerICI/premessa premessa@noreply.github.com Cc: Natalia Sigal nsigal@stanford.edu, Author author@noreply.github.com Subject: Re: [ParkerICI/premessa] error while debarcoding (#13)

Hi Natalia,

Can you please share with me the data you are trying to debarcode so that I can reproduce and fix the issue on my system?

Thanks

Federico

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ParkerICI/premessa/issues/13#issuecomment-387230608, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AlQQQ8Z0NU9xJDDFpTd6noZgqmMZG0XZks5twM_MgaJpZM4T1Ywl.

CNicholasMDA commented 6 years ago

I too am having this issue, with parameters set at separation of 0.3 and MD at 30. I will try Natalia's modifications in a few minutes, but was wondering if there has been any new insight into this issue/error? Thank you all! -Courtney

UPDATE: separation of 0.1 and MD of 15 seemed to work in my case...

pfgherardini commented 6 years ago

I have fixed the problem in the latest release. The error was due to the fact that some samples contained only 1 or 2 cells, as the corresponding barcoding combinations were not used.

Thanks for reporting!