globaltest protocols

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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

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Publication for globaltest

globaltest in pipelines

 (3)
2014
PMCID: 4297300
PMID: 25502872
DOI: 10.1007/s00251-014-0819-9

[…] the convest procedure of the limma r/bioconductor package (langaas et al. ) to estimate the proportions of peptides with a real difference between the dq types. in the second approach, we used the globaltest of the r/bioconductor package (goeman et al. ) to obtain p values for overall dq type differences. the histograms of z scores were generated by the method locfdr (efron )., binding motifs […]

2011
PMCID: 3078834
PMID: 21453500
DOI: 10.1186/1755-8794-4-29

[…] web applications, such as kegg (kyoto encyclopaedia of genes and genomes) [] or amigo [], were tested for differential expression between groups with high and low hormone concentration using globaltest []. the table in additional file lists all the 56 gene sets included in the analysis. the gene sets fulfilling the criteria p < 0.05, fdr <0.25, and comparative p < 0.20 […]

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

[…] r []. the tests used were the wilcoxon test as implemented in the limma package (version 2.14.5 [,]), fisher's exact test [] and kolmogorov smirnoff implemented in the topgo (version 1.8.1. []), and globaltest [,] 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 […]


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globaltest in publications

 (37)
PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] of base gse methods to rank biologically relevant gene sets. the current version of the egsea package utilizes the analysis results of up to twelve prominent gse algorithms that include: ora , globaltest , plage , safe , zscore , gage , ssgsea , padog , gsva , camera , roast and fry . the ora, gage, camera and gsva methods depend on a competitive null hypothesis which assumes the genes […]

PMCID: 5596581
PMID: 28837150
DOI: 10.1038/cddis.2017.398

[…] fitting a linear model using the limma package in r., , in order to identify pathways that are differentially regulated between 2d and 3d (static and bioreactor system) cell cultures, we applied a globaltest. this test evaluates gene ontology (go) terms (http://www.geneontology.org/) of the ‘biological process’ ontology., in addition, we sorted the regulated genes with the go term ‘autophagy’ […]

PMCID: 5530347
PMID: 27974301
DOI: 10.1136/annrheumdis-2016-210373

[…] language after quality checks using illumina beadstudio analysis software (illumina). intensity values were normalised and absence of large-scale between-chip effects was confirmed using the globaltest-package. probes that were not optimally measured were removed (detection p>0.05 in more than 50% of the samples). all comparisons of the differential normalised probe expression levels […]

PMCID: 5408797
PMID: 27694195
DOI: 10.1093/bioinformatics/btw623

[…] a variety of ways using simple statistics (e.g. the mean or sum of the statistics across all genes in a set) or more complicated approaches. linear models are widely used for this purpose (), as in globaltest (), camera (), fry and roast () and allow multiple covariates to be included in the analysis. several methods quantify gene set scores for each sample independently rather […]

PMCID: 4752453
PMID: 26870956
DOI: 10.1371/journal.pone.0148818

[…] using kernel-based orthogonal projections to latent structures (k-opls) []. from the four significant gene sets, we selected individual gene based on p-values and expression directions using the globaltest r package [, , ]. distinct from other meta-analysis, we selected individual markers which can explain the mechanisms underlying tumor stem-like breast cancer cells by applying gene set […]


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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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