metaMA protocols

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metaMA specifications

Information


Unique identifier OMICS_03524
Name metaMA
Alternative name meta-analysis for MicroArrays
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 3.0
Computer skills Advanced
Version 3.1.2
Stability Stable
Requirements
limma, GEOquery, org.Hs.eg.db, VennDiagram, hgu95av2.db, annaffy, R(≥3.1.2), SMVar, hgu133plus2.db, hgu133a.db
Maintained Yes

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Publication for meta-analysis for MicroArrays

metaMA in pipelines

 (2)
2017
PMCID: 5450516
PMID: 28587396
DOI: 10.3892/etm.2017.4378

[…] (r-project.org) was used to identify the differently expressed probe sets between ias and controls using the two-tailed student's t-test and p-values of individual microarray studies were obtained. metama package in r (r-project.org) was used to combine p-values from multiple microarray studies and false discovery rate (fdr) was calculated for multiple comparisons using the benjamini & […]

2012
PMCID: 3335030
PMID: 22536322
DOI: 10.1371/journal.pone.0034247

[…] was in all cases performed from raw data in.cel files using the rma method with background correction, and differential expression was analysed using limma (linear models for microarray data) . the “metama” package in r was used to perform statistical meta-analysis. the gather web tool was used to identify whether any lists of differentially expressed rnas were enriched for the targets […]


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metaMA in publications

 (14)
PMCID: 5812227
PMID: 29439675
DOI: 10.1186/s12872-018-0766-8

[…] were screened, which was shown in table .table 1p patients, n normal individual, p patients, n normal individual, raw expression data of aaa patients in this study were downloaded. limma and metama packages were used to identify the degs. and the inverse normal method was used to combine the p value in metama. the false discovery rate (fdr) was performed for multiple testing corrections […]

PMCID: 5779953
PMID: 28990066
DOI: 10.3892/mmr.2017.7711

[…] and normal control (nc) groups were selected. in addition, the selected datasets were the expression profile of whole-genome sequencing and were normalized or original., the present study used the metama package in r version 3.2.3 to combine data from multiple microarray datasets and obtained the individual p-values (). degs in glaucoma compared with nc were identified with false discovery […]

PMCID: 5603565
PMID: 28924174
DOI: 10.1038/s41598-017-12087-y

[…] effects model rather than a fixed effects model when the between-study heterogeneity based on cochran’s q test was significant. this method is based on the moderated es and was performed using the metama package. the two-way hierarchical clustering analysis of degs were conducted by the gplots package in the r software., to explore the functions of the identified degs, go and kegg pathway […]

PMCID: 5450516
PMID: 28587396
DOI: 10.3892/etm.2017.4378

[…] (r-project.org) was used to identify the differently expressed probe sets between ias and controls using the two-tailed student's t-test and p-values of individual microarray studies were obtained. metama package in r (r-project.org) was used to combine p-values from multiple microarray studies and false discovery rate (fdr) was calculated for multiple comparisons using the benjamini & […]

PMCID: 5290602
PMID: 28153032
DOI: 10.1186/s13045-017-0406-2

[…] ebayes function from “limma” package []. p value was adjusted by the benjamini-hochberg method []. for each gene in each study, we then calculated the effect size using the effectsize function from “metama” package []. the unbiased effect size and its variance were combined across multiple studies using the directescombi function. p value was calculated from the combined statistics using normal […]


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metaMA institution(s)
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; Biomathematics and Statistics, Rowett Institute of Nutrition and Health, University of Aberdeen, Scotland, UK
metaMA funding source(s)
Scottish Government Rural and Environment Research and Analysis Directorate (RERAD)

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