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Most people should have one folder per month (2014-03 etc).
In case of replicates, a list of bootstrap folders can be provided for each condition (one folder per replicate, normally with an equal number of bootstrap samples) - IsoDE will automatically merge the folders for the replicates to get a combined folder per condition, then perform the analysis as in the case without replicates.
Use one folder per class; if you mix up your class materials, you'll create more work later when you need to study.
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