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 <email@example.com>, Xiangli Zhang <firstname.lastname@example.org>|
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