AltAnalyzeStatistics modified by Anonymous

Anonymous — Sat, 01 Feb 2014 01:06:24 -0000

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