Building an analysis plan
Before inspecting outcomes, write the question, dataset, variables, preprocessing, baseline, method, metric and expected visualization.
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Before inspecting outcomes, write the question, dataset, variables, preprocessing, baseline, method, metric and expected visualization. Plan splits at the independent biological unit and preserve a test set for final evaluation. A baseline reveals whether the proposed method adds value. Distinguish exploratory changes from prespecified choices in the final report.
Worked example
For synthetic expression data, plan a patient-level split, median imputation learned on training data, a majority baseline, logistic classification, sensitivity and a per-gene distribution plot.