ELBOW: ELBOW - Evaluating foLd change By the lOgit Way

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ELBOW")
AuthorXiangli Zhang, Natalie Bjorklund, Graham Alvare, Tom Ryzdak, Richard Sparling, Brian Fristensky
Bioconductor views GeneExpression Microarray MultiChannel OneChannel RNASeq Sequencing Software Technology TwoChannel
Date of publicationNone
MaintainerGraham Alvare <alvare@cc.umanitoba.ca>, Xiangli Zhang <justinzhang.xl@gmail.com>
Licensefile LICENSE
Version1.12.0

View on Bioconductor

Functions

analyze_elbow Man page
do_elbow Man page
do_elbow_rnaseq Man page
EcoliMutMA Man page
EcoliWT Man page
elbowlib Man page
elbow_variance Man page
extract_working_sets Man page
get_elbow_limma Man page
get_pvalue Man page
GSE20986_design Man page
GSE20986_eset_exprs Man page
null_variance Man page
pkg_elbowlib Man page
pkg_elbowlib-package Man page
plot_dataset Man page
plot_elbow Man page
replicates_to_fold Man page
yeast_nbinomTest_results Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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