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