Background
All the files within a panel need to have the same collection of channels and reagent names. If this condition isn't met, a panel/channel conflict will result. For background on the concept of panels in Cytobank and vocab used in this article, see the overview article for panels and channels
When a panel/channel conflict is present in an experiment, it will be called out with an obvious banner that says, "There are currently panels that contain conflicting channels. These conflicts must be resolved before illustrations may be drawn."
(the panel channel conflict message. Click the link to navigate to the panel setup page and resolve conflicts. Clicking the hyperlink will navigate to the correct page)
Resolving Panel/Channel Conflicts
The types of conflicts and the path to resolve them can be divided into a small number of cases:
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Conflict on a channel name due to a typo or case change in the reagent name (e.g. "CD33" vs "cd33")
In this case, the files should be kept in the same panel and the channel name standardized using the resolve dialog.
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Conflict on the reagent channel name because the files have different markers (e.g. "pSTAT3" and "pp38")
One solution is to create another panel for the disagreeing files.
Another solution is to use the resolve dialog to choose a name that is standardized across all files on the channel in question. Name the channel something that represents both original channels, e.g., "marker A or marker B". Which marker is being displayed can then be sorted out in downstream analysis. This allows the use of a single Cytobank panel instead of multiple.
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Conflict due to difference in number of channels between files
The conflicting files have to be moved to different panels. Simply renaming channels (as described above) will not work in this situation because some files do not even have the channel in question. Instead, use the resolve dialog to move the files to an existing or new panel. Alternatively, move the files to a different panel manually.
Note, if you ultimately want the files in the same panel but they have a different number of channels, create a support request for assistance adjusting the number of channels in the files.
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Conflict due to difference in short name / detector name between files (e.g. "FL1" vs "FL-1")
Sometimes a conflict can emerge between samples that were acquired with the same panel but a conflict exists on the instrument channel name (aka "detector name", "short channel name"). The same reagent / marker is tagged on both channels, but the un-editable portion of the name is different. In this situation the files must be moved to different panels. To ultimately combine the files into the same panel, the files themselves must be edited or re-exported such that the short channel name is the same among files. This can be achieved using the Edit Channel feature described below.
Edit Channel feature
In the Cytobank platform, the Edit channel option can be used to resolve panel/channel conflicts arising from several mismatches in number of channels or differences in short name/detector name among different files that need to be analyzed together.
To access this feature, navigate to Assign panels page accessible from the File section present in the top blue navbar, and click on Edit channels button on the top right. A setup section will appear; click on the grey field next to the plus sign to select which action you want to perform.
You can use this feature to:
- Remove a channel
- Rename a channel to "new name"
- Add a new channel named "new name" (full of zeroes)
Depending on your selection, the platform will let you choose which channel you want to remove/rename from a dropdown list, and/or in which files. You will also have to define the new name for the rename option and add the new channel option.
Once you have completed your selections, you can click on Confirm change; a pop-up window with a summary that consolidates all commands into "sets of changes" will appear. Click Submit to proceed with the task: upon completion, it will produce a set of new files, while the old ones will be marked by "[pre-edited]" appended.
The platform will do a smart check on both the old and new files and move them to already existing panels in case there is a perfect match or create new panels in case of conflicts.
Importantly, all sample tags and file categorization (experimental, other control, or compensation) will be copied from the old file to the new file.
A record of all channels edit tasks will appear on the experiment summary page under the section called Channel-editing tasks and this history will be cloned if "clone analyses" is selected during cloning steps in the platform.
Importantly, when channels are renamed or removed, references in file-internal compensation matrices are updated accordingly.
For Research Use Only. Not for use in diagnostic procedures.