CyTOForum

Posted: **Sat May 02, 2020 9:08 pm**

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

Posted: **Sun May 03, 2020 3:12 am**

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).

Posted: **Sun May 03, 2020 12:09 pm**

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.

Posted: **Sun May 03, 2020 1:05 pm**

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

Posted: **Sun May 03, 2020 1:32 pm**

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.

CyTOForum

Edit/delete detector names in CyTOF FCS files?

Edit/delete detector names in CyTOF FCS files?

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

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

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

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