globaltest protocols

View
description
globaltest computational protocol

globaltest specifications

Information


Unique identifier OMICS_02084
Name globaltest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 5.34.1
Stability Stable
Requirements
AnnotationDbi, methods, KEGG.db, graphics, Biobase, MASS, survival, GO.db, org.Hs.eg.db, vsn, annotate, Rgraphviz, GSEABase, golubEsets, boot, hu6800.db, lungExpression, penalized, gss, rpart
Maintained Yes

Versioning


Add your version

Documentation


Publication for globaltest

globaltest IN pipelines

 (5)
2014
PMCID: 4232707
PMID: 25366961
DOI: 10.1186/s12859-014-0349-3

[…] beyond the mean z-score. stouffer’s p-value combination method was applied here as it is more powerful for the consensus alternative than say fisher’s p-value combination test [36] or goeman’s globaltest [6], see discussions in [24]. finally, multiplicity adjusted gene set p-values for each bp term were calculated using the short focus level procedure, with the root bp go term (go:0008510) […]

2009
PMCID: 2712751
PMID: 19615121
DOI: 10.1186/1753-6561-3-S4-S8

[…] tests used were the wilcoxon test as implemented in the limma package (version 2.14.5 [10,11]), fisher's exact test [12] and kolmogorov smirnoff implemented in the topgo (version 1.8.1. [13]), and globaltest [14,15] implemented in the globaltest package (version 4.12.0). for the fisher's exact test a predefined adjusted p-value of 0.05 was chosen to be the cutoff for individual […]

2009
PMCID: 2712751
PMID: 19615121
DOI: 10.1186/1753-6561-3-S4-S8

[…] implemented in the limma package (version 2.14.5 [10,11]), fisher's exact test [12] and kolmogorov smirnoff implemented in the topgo (version 1.8.1. [13]), and globaltest [14,15] implemented in the globaltest package (version 4.12.0). for the fisher's exact test a predefined adjusted p-value of 0.05 was chosen to be the cutoff for individual oligonucleotides to be differentially expressed. […]

2009
PMCID: 2712751
PMID: 19615121
DOI: 10.1186/1753-6561-3-S4-S8

[…] package (version 4.12.0). for the fisher's exact test a predefined adjusted p-value of 0.05 was chosen to be the cutoff for individual oligonucleotides to be differentially expressed. except for the globaltest, the result of statistical hypothesis testing (t-statistics or p-value) for the oligonucleotides was used as input data for the gene set analyses. the globaltest uses the expression data […]

2009
PMCID: 2712751
PMID: 19615121
DOI: 10.1186/1753-6561-3-S4-S8

[…] expressed. except for the globaltest, the result of statistical hypothesis testing (t-statistics or p-value) for the oligonucleotides was used as input data for the gene set analyses. the globaltest uses the expression data directly when testing gene sets and the corresponding p-values were computed using either the asymptotic distribution or permutations [14]. the gene set testing […]

globaltest institution(s)
Department of Medical Statistics, Leiden University Medical Center, Leiden, Netherlands; Mathematical Institute, Leiden University, Netherlands; Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands

globaltest reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review globaltest