How does ROSALIND calculate GSA Scores and enrich for pathway analysis for nCounter data?

Gene Set Analysis (GSA) is incorporated into ROSALIND to summarize the global significance score and the directed global significance score. GSA summarizes the change in regulation within each defined gene set relative to the baseline. More information on GSA algorithm details can be found on page 56 of the nCounter® Advanced Analysis 2.0 User Manual.

Additional ROSALIND enrichment is calculated for gene sets as defined in multiple databases including WikiPathways, REACTOME, MSigDB, and Gene Ontology. Enrichment is calculated in reference to the background set of genes, or all genes in the panel. FDR adjustment and p-Elim pruning scores are provided when appropriate.

For miRNA nCounter data ROSALIND analyzes the top targeted gene predictions, validated genes, and related drugs and diseases using the multiMiR R library. multiMir referenced multiple database like miRecords, MIRTarbase, miRDB, TargetScan, and miRanda to report enrichment scores.