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ELBOW (version 1.8.0)

ELBOW - Evaluating foLd change By the lOgit Way

Description

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.

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Version

Version

1.8.0

License

file LICENSE

Maintainer

Graham Alvare

Last Published

February 15th, 2017

Functions in ELBOW (1.8.0)

EcoliMutMA

Escherichia coli str. K-12 substr. MG1655 - EcoliMutMA (GSM576640-45 mutant -- G3.2 mutant of E.coli EcNR1, no isobutanol)
plot_elbow

plots Elbow curve data.
GSE20986_design

Comparative Gene Expression Profiling of HUVEC and Ocular Vascular Endothelial Cells (GEO database entry GSE20986) microarray design data file
EcoliWT

Escherichia coli str. K-12 substr. MG1655 - EcoliWT (GSM576634-39 WT -- WT E.coli EcNR1, no isobutanol)
GSE20986_eset_exprs

Comparative Gene Expression Profiling of HUVEC and Ocular Vascular Endothelial Cells (GEO database entry GSE20986) microarray data eset expression values - SUBSET
do_elbow_rnaseq

Calculates fold values from an MArrayLM object.
yeast_nbinomTest_results

Pre-processed Yeast sample RNA-seq data
analyze_elbow

extracts all elbow statistics and plots and elbow curve.
ELBOW

Evaluating foLd change By the lOgit Way
extract_working_sets

extract the initial and final conditions from a table.
plot_dataset

plots data to see if it matches an elbow distribution.
elbow_variance

calculates the variance for the upper and lower limits of an Elbow curve
do_elbow

calculates the upper and lower elbow cut-off fold-values
null_variance

determines the variance for a null Elbow curve
replicates_to_fold

calculates fold values from a table of experimental data
get_pvalue

The calculated $\log\chi^2$ p-value for the fit of the elbow curve to the model.
get_elbow_limma

Calculates fold values from an MArrayLM object.