QuSAGE

qusage, or Quantitative Set Analysis of Gene Expression, is a significant advancement in gene enrichment analysis. It provides a functional interpretation of genome-wide expression data. Traditional methods like GSEA and CAMERA have limitations, such as inflated error rates. GSEA uses complex permutations to maintain gene-gene correlations, while CAMERA corrects these correlations through a variance inflation factor. However, neither method provides confidence intervals or supports post hoc comparisons.

qusage stands out by directly incorporating inter-gene correlations into its computational framework, a feature that enhances the accuracy of variance inflation factor estimation. Unlike its predecessors, qusage quantifies gene-set activity using a complete probability density function. This unique approach enables the extraction of P-values, allows for the generation of confidence intervals, and facilitates post hoc analyses while preserving statistical integrity.