Run a group analysis

The Group Analysis function enables you to look at proteins or peptides from the analysis results and apply a statistical test between two comparison groups. You can further filter or exclude samples from the dataset to focus in your analysis.

Before you can run a group analysis, you must first select a single completed analysis that has at least one category with at least two groups.

You can select only one completed analysis for a group analysis. You can not perform a group analysis on more than one analysis results at a time.

To run a group analysis:

  1. On the Analyses page, select a completed analysis to load the results data.

  2. Scroll to the Group Analyses pane and select Run group analysis.

    The Group Analysis Setup screen appears.

  3. In the Data Type area, select either Proteins (default) or Peptides.

  4. In the Statistical Test area, select either T test (default) or Wilcoxon.

    For more information on statistical tests, select Compare statistical tests or see About group analyses.

  5. In the Select Comparison Groups area, select a category from the drop-down list, and then select the two groups you want to compare.

    The two groups must be in the same category. When you choose a category, the groups drop-downs show the groups within the selected category. If only the category contains only one group, you will not be able to complete the group analysis.

    The groups derive from the data in the selected Condition and custom columns from the sample description file or from adding custom columns in the samples table on the Projects and Plates pages.

  6. (Optional) In the Filter Comparison Groups area, you can further refine your group analysis by selecting a category that includes the subgroups you want to filter. Then select groups within that category to include in the group analysis.

    If you select a category but do no select subgroups, data from all subgroups will be included in the analysis.

    For more information select Learn more or see About group analyses.

  7. (Optional) Select + Add filter category to further refine your group analysis by filtering the dataset using other sample metadata or subgroups. Select subgroups within that category to include in the group analysis. If no subgroups are selected, data from all subgroups will be included in the analysis.

    You can add as many additional subgroup categories and subgroups as the analysis results contain.

  8. (Optional) In the Excluded Individual Samples area, select a check box in front of each sample you want to exclude from the analysis.

  9. (Optional) In the Missing Value Filtering area, adjust the threshold values to filter for missing values in each comparison group. You can enter values in the Number of samples or Percent of samples boxes.

    The default settings for the missing value filters ensure that the statistical test you have chosen will be statistically valid. However, you may choose to select different thresholds based upon the needs of your analysis.

    The most restrictive thresholds selected will be applied.

    As you enter values, the information description above the boxes updates to include the values you enter, and the number of proteins or peptides remaining after the filter is applied appears at the bottom of the Missing Value Filtering area.

    When setting thresholds:

    • Consider the size of your dataset and the variability of protein detection.

    • Higher thresholds will result in more stringent filtering, potentially excluding more data but increasing reliability.

    • Lower thresholds will include more data but may introduce more variability.

  10. (Optional) If you want to add single-group filter thresholds, select + Add single group filter thresholds in the Missing Value Filtering area.

    Additional Number of samples or Percent of samples boxes appear. Enter values to apply these filters.

    To remove the single-group threshold filter, select - Remove single group filter thresholds in the Missing Value Filtering area

  11. (Optional) In the Normalization Method area, select None - log10 (unnormalized) or Median Normalization.

    For more information, select Learn more or see About group analyses.

  12. Select Run group analysis to run the analysis.

    The completed analysis data appears on the Analyses page in the Group Analyses area where you can: