Yes. Data preparation should happen at the Dataset level before a workflow is started. All filenames, metadata, and feature names will be present in all workflows in the same state they are within the Dataset. That means any metadata or feature name corrections you make after starting a workflow will carry through, but it's cleaner to resolve misalignments and set metadata first. The four videos in this series cover the full preparation sequence in order.
FCS files contain their own embedded metadata: entries that describe the file itself, the time of acquisition, information about the instrument and each detector, etc. OMIQ metadata is separate: it's the experimental or clinical context you add to your files, such as treatment group, patient ID, or timepoint. The FCS Metadata Import above video shows how to pull relevant values from the FCS file's embedded data into OMIQ metadata, so you don't have to enter them manually.
No. Editing metadata or feature names does not alter the underlying raw data. Raw data are never altered within OMIQ. All operations on data are stored as "layers" on top of the raw data.
Having different feature names across different FCS files can prevent proper analysis and be very hard to correct, but with OMIQ, this can be solved easily. OMIQ handles misaligned, extra, or misordered features between files. The Misaligned Missing Features video above walks through how OMIQ identifies and highlights these conflicts so you can resolve them before analysis.
Setting metadata supports a number of special OMIQ functionalities, including file searching, figure generation, and statistical analysis. You can upload and begin exploring data without it, but metadata is needed for grouping files, running differential analysis between conditions, and building meaningful figures. If you're running a simple single-sample analysis, it's optional. For any multi-sample or comparative experiment, it's not.
