ELBOW: ELBOW - Evaluating foLd change By the lOgit Way

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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
Date of publication
None
Maintainer
Graham Alvare <alvare@cc.umanitoba.ca>, Xiangli Zhang <justinzhang.xl@gmail.com>
License
file LICENSE
Version
1.10.0

View on Bioconductor

Man pages

analyze_elbow
extracts all elbow statistics and plots and elbow curve.
do_elbow
calculates the upper and lower elbow cut-off fold-values
do_elbow_rnaseq
Calculates fold values from an MArrayLM object.
EcoliMutMA
Escherichia coli str. K-12 substr. MG1655 - EcoliMutMA...
EcoliWT
Escherichia coli str. K-12 substr. MG1655 - EcoliWT...
ELBOW-package
Evaluating foLd change By the lOgit Way
elbow_variance
calculates the variance for the upper and lower limits of an...
extract_working_sets
extract the initial and final conditions from a table.
get_elbow_limma
Calculates fold values from an MArrayLM object.
get_pvalue
The calculated \logchi^2 p-value for the fit of the elbow...
GSE20986_design
Comparative Gene Expression Profiling of HUVEC and Ocular...
GSE20986_eset_exprs
Comparative Gene Expression Profiling of HUVEC and Ocular...
null_variance
determines the variance for a null Elbow curve
plot_dataset
plots data to see if it matches an elbow distribution.
plot_elbow
plots Elbow curve data.
replicates_to_fold
calculates fold values from a table of experimental data
yeast_nbinomTest_results
Pre-processed Yeast sample RNA-seq data

Files in this package

ELBOW/DESCRIPTION
ELBOW/LICENSE
ELBOW/NAMESPACE
ELBOW/R
ELBOW/R/elbowlib.R
ELBOW/build
ELBOW/build/vignette.rds
ELBOW/data
ELBOW/data/EcoliMutMA.tab.xz
ELBOW/data/EcoliWT.tab.xz
ELBOW/data/GSE20986_design.tab.xz
ELBOW/data/GSE20986_eset_exprs.tab.xz
ELBOW/data/datalist
ELBOW/data/yeast_nbinomTest_results.tab.xz
ELBOW/inst
ELBOW/inst/doc
ELBOW/inst/doc/Elbow_tutorial_vignette.R
ELBOW/inst/doc/Elbow_tutorial_vignette.Rnw
ELBOW/inst/doc/Elbow_tutorial_vignette.pdf
ELBOW/inst/extdata
ELBOW/inst/extdata/EcoliMutMA.csv
ELBOW/inst/extdata/phenodata.txt
ELBOW/inst/extdata/yeast_sample_data.txt
ELBOW/man
ELBOW/man/ELBOW-package.Rd
ELBOW/man/EcoliMutMA.Rd
ELBOW/man/EcoliWT.Rd
ELBOW/man/GSE20986_design.Rd
ELBOW/man/GSE20986_eset_exprs.Rd
ELBOW/man/analyze_elbow.Rd
ELBOW/man/do_elbow.Rd
ELBOW/man/do_elbow_rnaseq.Rd
ELBOW/man/elbow_variance.Rd
ELBOW/man/extract_working_sets.Rd
ELBOW/man/get_elbow_limma.Rd
ELBOW/man/get_pvalue.Rd
ELBOW/man/null_variance.Rd
ELBOW/man/plot_dataset.Rd
ELBOW/man/plot_elbow.Rd
ELBOW/man/replicates_to_fold.Rd
ELBOW/man/yeast_nbinomTest_results.Rd
ELBOW/vignettes
ELBOW/vignettes/175_mean.jpg
ELBOW/vignettes/Elbow_tutorial_vignette.Rnw
ELBOW/vignettes/bad_density_plot.jpg
ELBOW/vignettes/biodata_nonsymmetry.jpg
ELBOW/vignettes/density_plot_sample.jpg
ELBOW/vignettes/elbow_annotated.jpg
ELBOW/vignettes/elbow_man.jpg
ELBOW/vignettes/elbow_on_nonsymmetric.jpg
ELBOW/vignettes/elbow_pvalue.jpg
ELBOW/vignettes/elbows_circled.jpg
ELBOW/vignettes/flat_initial.jpg
ELBOW/vignettes/initial_flat_no_pvalue.jpg
ELBOW/vignettes/logit_inverted.jpg
ELBOW/vignettes/logit_standard.jpg
ELBOW/vignettes/logit_standard_full.jpg
ELBOW/vignettes/method_comparison.jpg
ELBOW/vignettes/no_elbow.jpg
ELBOW/vignettes/normalize_data.jpg
ELBOW/vignettes/null_graph.jpg
ELBOW/vignettes/prepare_columns.jpg
ELBOW/vignettes/qtpcr-vs-omic.jpg
ELBOW/vignettes/replicate_probe_cross_table.jpg
ELBOW/vignettes/replicates_table.jpg
ELBOW/vignettes/save_csv.jpg
ELBOW/vignettes/standard_elbow.jpg
ELBOW/vignettes/symmetry_about_zero.jpg
ELBOW/vignettes/tail_density.jpg
ELBOW/vignettes/typical_elbow.jpg