metaArray protocols

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metaArray specifications

Information


Unique identifier OMICS_01986
Name metaArray
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for metaArray

metaArray in pipeline

2014
PMCID: 3979809
PMID: 24714365
DOI: 10.1371/journal.pone.0094325

[…] package ., for each cancer training/validation dataset, we normalized the gene expression level into the scale of [−1, 1] by poe (probability of expression) algorithm , implemented in the metaarray library of the r statistical package . based on the gene expression and clinical outcome data from the training dataset, we can assign a wald statistic generated by univariate cox […]


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metaArray in publications

 (7)
PMCID: 5301337
PMID: 28183295
DOI: 10.1186/s12885-017-3103-1

[…] a non-parametric ‘rank product’ method [, ]. rankprod is among the most popular tool which utilizes a non-parametric statistical method and outperforms other meta-analysis methods, including metaarray [], genemeta [], and mama [], by ranking the differentially expressed genes based on false discovery rate. matched diagnosis and relapse samples represent the most ideal biological samples […]

PMCID: 5399965
PMID: 28491277
DOI: 10.5256/f1000research.11275.r19356

[…] from different platforms is that some genes might be captured with varying quality across platforms. it is unclear what was done to identify problematic probe sets or genes. various r packages (e.g. metaarray) for example calculate integrative correlation scores. these scores identify probe sets which behave differently across platforms in terms of co-expressed genes. another challenge […]

PMCID: 4746218
PMID: 26900390
DOI: 10.1186/s13637-015-0034-5

[…] de via distance synthesis (deds) [] to aggregate multiple de measurements. the performance of mdeds was compared with existing meta-analysis methods, such as fisher’s inverse chi-square, genemeta, metaarray, rankprod, and naïve meta-methods, using a simulation study and two case studies []. the results mostly showed better performance for mdeds, while some cases favored the fisher’s inverse […]

PMCID: 4141256
PMID: 25146220
DOI: 10.1038/srep06107

[…] in stage ii tumor, we further included an additional lung cancer dataset (gse41271) here. we merged the subjects of stage ii from three independent cohorts (lung1, lung2, and gse41271) using the “metaarray” package in bioconductor (see for details). we found that n39-positive patients (with stage ii tumor) exhibited a significantly increased risk (1.68-fi, p = 0.049 by univariate cox […]

PMCID: 3979809
PMID: 24714365
DOI: 10.1371/journal.pone.0094325

[…] package ., for each cancer training/validation dataset, we normalized the gene expression level into the scale of [−1, 1] by poe (probability of expression) algorithm , implemented in the metaarray library of the r statistical package . based on the gene expression and clinical outcome data from the training dataset, we can assign a wald statistic generated by univariate cox […]


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metaArray institution(s)
Department of Statistics and Huck Institute for Life Sciences, Penn State University, University Park, PA, USA

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