There are four concepts related to data in the workbench.
There is no one-to-one correspondence between FCS files, plates, or experiments. Many combinations are possible, depending on the task at hand. The following image shows some of the more common cases. The usage and workflows for each one is described below.
Usage: most frequent case.
Procedure: read an FCS file, the plate will appear automatically, select the samples of interest, create an experiment.
Usage: if two sets of samples were scanned on different days, but it were desired to view them and process them as one set.
Procedure: At the time the FCS file browser is open, select more than one FCS file before clicking "open". The wells from both files will appear on the plate. Form an experiment as usual.
A similar result can be accomplished by reading one FCS file into one plate, reading the other FCS file into a different plate, forming experiments on both plates, and then merging the experiments. The plates, however, will remain distinct.
Usage: if the first scan of the plate did not read enough particles, and a second scan is performed. Both reads of each well can be combined into a single well.
Proceed as if they were non-overlapping. However, when the workbench notices that data from two incoming samples have the same well name, it will prompt you if it is ok to merge them. If you accept, the FCS records from both files will be combined into the same well on the plate.
If you refuse, both samples will be present separately, and will not appear in the plate view. They will be visible in the plate list view instead.
Normally you would only want to combine FCS files onto a plate if they were derived from the same barcoded batch.
Usage: when a plate combines wells with particles from different barcoded batches. It is essential to separate out the wells with different barcodes, because the workbench converts FCS events to particles using all the samples on a plate. If one barcode is a 70-plex and the other is a 35-plex, the results are unpredictable.
Procedure: after reading the FCS file, select a group of samples on the plate, and use the popup to create a new plate. Repeat for each group of samples to be treated separately. When finished, you generally will want to discard the original combination plate, since each sample will have two "owners", the combination plate, and the subset plate. Then, for each subset plate, select the appropriate PLX file using the top menu. Finally, form experiments on each of the subset plates.
Usage: a set of samples is too large to fit on a single plate.
Procedure: read each 96-well FCS file into one plate, and form an experiment. When all experiments are created, merge them into a single super-experiment. You may want to delete all the single plates after that, since they will clutter the experiment table.
The lack of correspondence between a plate and an experiment can be confusing. However it is an inevitable consequence of the fact that not every experiment can be represented as a plate (e.g. an experiment with 400 samples, generated by collecting samples from multiple plates). Some examples that may help clarify the difference are
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