Nested design involves measurements taken repeatedly from the same biological source across multiple time points—for example, drawing blood from the same patients for several consecutive days. Using nested design is potentially a more sensitive way to spot trends.

Procedure

  1. On the Study Definition page, create the study factors to assign to the quantification channels. See Add the study factors to the study.
  2. The following example assigns study factors 1, 2, and 3 to the quantification channels.
  3. Study factors assigned to the quantification channels
    Study factors assigned to the quantification channels
  4. On the Input Files page, assign the study factors to the quantification channels:
  5. Select the gray arrow to the left of the first replicate row.
  6. Select all the quantification channels used for a given replicate.
  7. Right-click the Replicate column, and select Set Replicate To > study_factor_number.
  8. The following example assigns study factor Bio Rep 2 to the replicate 2 dataset.
  9. Assignment of study factors to quantification channels in a nested design
    Assignment of study factors to quantification channels in a nested design
  10. Select the Grouping & Quantification tab.
  11. The following figure shows three biological replicates that are being remeasured multiple times. The Generated Ratios pane of the Grouping & Quantification page confirms that the design is nested.
  12. Generated Sample Groups page showing replicates in a nested design
    Generated Sample Groups page showing replicates in a nested design