CAnBioNet / TkNA

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Implement paired t-test #30

Closed macovskym closed 1 year ago

macovskym commented 1 year ago

To use a paired t-test, you must do the following:

  1. Create a CSV file for each experiment with the format:
    • First row containing the names of treatments
    • First column containing names for the pairings (can be empty)
    • Cells containing the names of samples as used in the experiment data tables

For example:

0wk 4wk 8wk
mouse1 sample4 sample48 sample74
mouse2 sample9 sample34 sample71
mouse3 sample14 sample38 sample65
  1. Add the paths to the pairing CSV files to metadata.json:
    ...
    "experiments": [
    {
        "name": "experiment1",
        ...
        "pairingsFile": "experiment1_pairings.csv"
    },
    {
        "name": "experiment2",
        ...
        "pairingsFile": "experiment2_pairings.csv"
    },
    ...
    ],
    ...
  2. Specify paired t-test in the config file:
    {
    ...
    "differenceMethod": "pairedttest",
    ...
    }
bruceamm commented 1 year ago

Allows user to calculate paired t-test, verified output in Excel (no errors or issues, AB/IS)