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How to Compare Sample Groups

Multi-Sample Session Specific

This feature is only available in multi-sample sessions.

This guide explains how to perform multi-sample cohort comparisons in CartoScope by grouping samples into contrast pairs, selecting statistical test models, and exploring differential expression metrics.

1. Assign Sample Labels

  • 1) Open Sample Drawer: Click the Sample button in the Top Bar to open the Sample Drawer.
  • 2) Assign Groups: In the Sample Label tab, assign each participating sample to Group 1 (e.g. Control) or Group 2 (e.g. Treated). Unassigned samples are excluded from calculations.

2. Configure Comparison Settings & Run Statistical Model

  • 1) Open Sample Compare Tab: Switch to the Sample Compare tab in the Sample Drawer.
  • 2) Select Test Method: Choose between Chi-Squared Test (fast contingency screening) or DESeq2-inspired Model (replicate-aware Negative Binomial testing).
  • 3) Select Multiple Testing Correction: Choose BH FDR (False Discovery Rate) or Šidák FWER (Family-Wise Error Rate).
  • 4) Run Contrast: Click Run Comparison to compute differential expression metrics.

3. Explore Results and Export Data

  • 1) Interactive Volcano Plot: Hover over gene data points to view \(\log_2\text{FC}\), raw \(p\)-values, FDR, and FWER values. Click any gene row or data point to highlight its spatial expression on the map.
  • 2) Export Results: Click Export Stats Table to download the differential expression statistics matrix as a CSV or TSV file.

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