Method comparison study requirements and dataset layout.
Use a column for each method (Method 1, Method 2); each row has the measurement by each method for an item (Subject).
Use multiple columns for the replicates of each method (Method 1, Method 2); each row has the replicate measurements by each method for an item (Subject).
Use a column for each method (Method 1, Method 2); each row has the measurements by each methods for an item (Subject), with multiple rows for replicates of each item.
Use a column for the measurement variable (Measured value), a column for the method variable (Method), and a column for the item variable (Subject); each row has the measurement for a method for an item (Subject), with multiple rows for replicates of each item.