How can I create a merged data file with equally-sized downsampled samples?

Sometimes, when running high-dimensional data analysis, multiple files must be merged together before performing a transformation/algorithm.

When file merging is necessary, it is often useful to use the same number of events for each representative data file, from either the full dataset or from a specific gate.

The steps below outline how to create a merged file that contains the same number of events from each dataset.

Note: for a more comprehensive pre-processing pipeline including data cleaning and scaling, please refer here instead.

How to create a merged file with the same number of events from each data file

1. Load one of the data files into the layout.

2. Create the gate that should be exported (if any). Please note that Data Specific gates will not be applied at export.

3. Create a pipeline and add the desired Downsampling step. Be sure to select all the parameters in the main pipeline body (unselected parameters will not be exported).

4. Create a merged file using Batch Export tool. Be sure to select the appropriate file format and compensation. Be sure to select the pipeline created in the previous step in the Export with transformation dialog. Do not select any gate in the Batch Export dialog (the gate selected in the pipeline, if any, will be automatically used). For more details on the Batch Export tool see here.

The exported files will contain the same number of events from the same gate from each data files.

A merged file created via the procedure above is depicted below (10,000 events have been taken from each of the 9 files of interest).

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