globaltest pipeline

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
Stability Stable
Maintained Yes

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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

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