ELBOW

ELBOW - Evaluating foLd change By the lOgit Way

Bioconductor version: Development (3.0)

Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.

Author: Xiangli Zhang, Natalie Bjorklund, Graham Alvare, Tom Ryzdak, Richard Sparling, Brian Fristensky

Maintainer: Graham Alvare <alvare at cc.umanitoba.ca>, Xiangli Zhang <zhangju at cc.umanitoba.ca>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ELBOW")

Citation (from within R, enter citation("ELBOW")):

Documentation

PDF R Script Using ELBOW --- the definitive ELBOW tutorial
PDF   Reference Manual
Text   LICENSE

Details

biocViews GeneExpression, Microarray, MultiChannel, OneChannel, RNASeq, Sequencing, Software, Technology, TwoChannel
Version 1.1.0
In Bioconductor since BioC 2.14 (R-3.1)
License file LICENSE
Depends R (>= 2.15.0)
Imports
Suggests DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ELBOW_1.1.0.tar.gz
Windows Binary ELBOW_1.1.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ELBOW_1.1.0.tgz
Mac OS X 10.9 (Mavericks) ELBOW_1.1.0.tgz
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