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EBarrays specifications


Unique identifier OMICS_20502
Name EBarrays
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 2.44.0
Stability Stable
methods, stats, graphics, Biobase, grDevices, lattice, cluster, R(>=1.8.0)
Maintained Yes




No version available



  • person_outline Ming Yuan

EBarrays citations


Robust volcano plot: identification of differential metabolites in the presence of outliers

BMC Bioinformatics
PMCID: 5896081
PMID: 29642836
DOI: 10.1186/s12859-018-2117-2

[…] lite identification techniques: three classical parametric approaches (t-test, FCROS, CVP), three nonparametric approaches (Wilcoxon test, K-W test, SAM) and three Bayesian approaches (BRIDGE, Limma, EBarrays). We also evaluate the performance of the proposed method using both artificially generated and experimentally measured metabolomics datasets in the absence and presence of outliers. Every me […]


Nuclear Phosphatidylinositol Phosphate Type I Kinase α Coupled Star PAP Polyadenylation Regulates Cell Invasion

PMCID: 5809686
PMID: 29203642
DOI: 10.1128/MCB.00457-17

[…] ompared with those for the control siRNA-treated samples, taken as baseline expression. Changes in expression were statistically analyzed using the empirical Bayes method implemented in the R package EBarrays, a publicly available statistical analysis system (http://www.r-project.org). We used the log-normal normal (LNN) expression model to calculate posterior probabilities of differential express […]


Robust Significance Analysis of Microarrays by Minimum β Divergence Method

Biomed Res Int
PMCID: 5551475
PMID: 28819626
DOI: 10.1155/2017/5310198

[…] other popular methods (ANOVA, SAM, LIMMA, KW, EB, GAGA, and BRIDGE), we used both simulated and real microarray gene expression datasets. We used five R packages of other methods such as samr, limma, EBarrays, gaga, and bridge. The performance measures AUC and pAUC were computed for each of the methods using ROC package. All R packages are available in the comprehensive R archive network (cran) or […]


RNA isolation from precision cut lung slices (PCLS) from different species

BMC Res Notes
PMCID: 5343379
PMID: 28274266
DOI: 10.1186/s13104-017-2447-6

[…] lain platform (www.genexplain-platform.com) to perform a principal component analysis (PCA). The geneXplain platform was further used to detect differentially expressed genes for all samples with the EBarrays workflow. […]


Construction of protein interaction network involved in lung adenocarcinomas using a novel algorithm

PMCID: 4998145
PMID: 27588126
DOI: 10.3892/ol.2016.4822

[…] e members of an array with length n were provided values ‘1,…, K’, where K is the total number of conditions. All microarrays and assays were placed in the same order as the n columns of X. An object EBarrays Pattern was used to define the equivalent coexpression/DC classes. Next, the function makeMyD() of biweight midcorrelation was used to the calculate intra-group associations for all p = m(m − […]


Modeling fibrosis using fibroblasts isolated from scarred rat vocal folds

PMCID: 4920689
PMID: 27111284
DOI: 10.1038/labinvest.2016.43
call_split See protocol

[…] ies. The resulting normalized data were clustered to check for consistency prior to formal analysis.Expression analysis was performed using an empirical Bayes approach as implemented in the R package EBarrays. A lognormal-normal moderated variance (LNNMV) model was fit to the data; parameter estimates were obtained via 20 iterations of an expectation-maximization (EM) algorithm: in all cases, conv […]


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