AltAnalyzeStatistics

Statistical Methods Implemented in AltAnalyze

AltAnalyze implements various previously described algorithms for gene expression quantification, differential gene expression, alternative exon expression and feature/pathway over-representation. These algorithms are implemented in the context of a rigorous exon/transcript annotation framework, based on data from Ensembl and UCSC mRNAs. Details on all of these methods is provided here.

In general, implemented methods include:

Gene Expression Analyses

• Robust Multichip Analysis (Affymetrix)
• Detection Above Background p-values (Affymetrix)
• Quantile normalization (RNASeq)
• RPKM (gene, exon, junction) (RNASeq)
• Geometric fold calculation
• Moderated and conventional two-sample tests and f-test
• Benjamini-Hochberg adjusted FDR test

Alternative Exon Analyses

• Reciprocal-junction analyses (ASPIRE, Linear regression)
• Alternative exon (splicing-index, FIRMA, MiDAS, adjusted f-tests)

Over-representation

• Fisher Exact Test
• Z score calculation
• Permutation-based p-values
• Benjamini-Hochberg adjusted FDR test

LineageProfiler analysis

• Pearson/Spearman's correlation
• Z score calculation