FAQ  •  Register  •  Login

Edit/delete detector names in CyTOF FCS files?

Forum rules
All comments are welcome. A civil tone is appreciated :-)
<<

sudhcha

Participant

Posts: 4

Joined: Tue Jul 24, 2018 8:37 am

Post Sat May 02, 2020 9:08 pm

Edit/delete detector names in CyTOF FCS files?

Hi Everyone,
I have two CyTOF experiments with different detector names/instrument channel names, and also with different numbers of detectors channels. I understand that one can change marker names in cytobank, but not the detector names. I was wondering if someone can suggest a R package to edit/detele detector names.
Thanks,
Sudhir
<<

dtelad11

Master

Posts: 119

Joined: Mon Oct 31, 2016 6:26 pm

Post Sun May 03, 2020 3:12 am

Re: Edit/delete detector names in CyTOF FCS files?

You can do this with the cytutils package:

https://github.com/ismms-himc/cytutils

Check out channelRename. It outputs a CSV spreadsheet where you can rename the "name" and "desc" field in the FCS file (corresponding to isotope and antibody names, respectively).
<<

sgranjeaud

Master

Posts: 79

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Sun May 03, 2020 12:09 pm

Re: Edit/delete detector names in CyTOF FCS files?

Hi,
cytutils and cytofcore and two interesting tools I like for doing this using R commands.
I got a tuto at http://impact-cyto.inserm.fr/harmoniser-des-panels/ (english script at the end).
If you are looking for a graphical user interface, Premessa is a very good alternative.
Have a look https://github.com/ParkerICI/premessa#p ... d-renaming
Best.
<<

avinash1

Participant

Posts: 14

Joined: Fri Jun 16, 2017 1:59 pm

Post Sun May 03, 2020 1:05 pm

Re: Edit/delete detector names in CyTOF FCS files?

Thanks El-ad and Samuel for your replies. Just curious if we can use the same tools to remove channels from the FCS files ? Regards Avi
<<

sgranjeaud

Master

Posts: 79

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Sun May 03, 2020 1:32 pm

Re: Edit/delete detector names in CyTOF FCS files?

I would say "read the doc!".

Here, what you will find in the usage section of the panel edit/rename tool of Premessa

The table begins with three special columns:
* Remove: if the box is checked the corresponding parameter is removed from all the files, and the row is grayed out
* Parameter: this column represent the parameter name ($PnN keyword). Initially it will be identical to the first column of row names, but this column is editable. You can edit this column if you want to change the parameter names in the output files.
* Most common: this column indicates what is the most common description value for that parameter, across all the files under analysis (i.e. the most common string across the row). Cells whose value differs from the value indicated in this column are displayed with a light pink background.


Before you ask for the opposite, cytofcore is useful if you want to add an empty channel. :)

Best.

Return to Forum requests and announcements

Who is online

Users browsing this forum: No registered users and 1 guest