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:
- 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.
- 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.
- 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.
- 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 uneditable 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 cannot be done in Cytobank, but Cytobank Support can offer guidance on ways to accomplish this workflow.