ArrayTools statistics

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ArrayTools specifications

Information


Unique identifier OMICS_02022
Name ArrayTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.40.0
Stability Stable
Requirements
limma, methods, stats, graphics, Biobase, utils, grDevices, affy, genefilter, Biobase(>=2.5.5), affydata, affy(>=1.23.4), R(>=2.7.0), xtable, R2HTML, affyPLM, gcrma, simpleaffy, annaffy, hugene10sttranscriptcluster.db
Maintained Yes

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Documentation


ArrayTools in publications

 (522)
PMCID: 5954140
PMID: 29765046
DOI: 10.1038/s41467-018-04244-2

[…] in accordance with the manufacturer’s instructions., the random variance t‐test was applied to identify genes differentially expressed between the two classes using biometric research branch (brb) arraytools (national cancer institute, bethesda, md). gene expression differences were considered statistically significant if the p‐value was less than 0.001. cluster analysis was performed […]

PMCID: 5961875
PMID: 29616846
DOI: 10.1089/acm.2017.0053

[…] statistically significant if their p-value was <0.05. p-values for significance were computed based on 1000 random permutations, at a significance level of each univariate test of 0.05 using brb-arraytools., to determine whether the drop in bp after the rr intervention was linked to specific antihypertensive changes in gene expression and pathophysiologic pathways, transcriptome […]

PMCID: 5885379
PMID: 29618380
DOI: 10.1186/s40425-018-0331-0

[…] for further analysis. in preliminary studies, the average intensity values from all initial 20 arrays were normalized simultaneously using an interquartile range transformation performed using brb-arraytools v4.5.0 developed by dr. richard simon and the brb-array tools development team (brb.nci.nih.gov/brb-arraytools). these preliminary arrays are presented in additional file : data file s1, […]

PMCID: 5895709
PMID: 29674952
DOI: 10.3389/fnmol.2018.00103

[…] and integrity and purity was determined by an agilent bioanalyzer and a nano-drop spectrophotometer. transcriptome analysis was performed using brbarraytoolsdeveloped by dr. richard simon and brb-arraytools development team. the data obtained in our microarray experiment were deposited at the geo website under accession number geo: gse111494. microarray data were further analyzed […]

PMCID: 5862949
PMID: 29563500
DOI: 10.1038/s41467-018-03556-7

[…] platforms (u133 v2.0). all data were normalized by using the robust multi-array average method. all patients had undergone cytoreductive surgery and subsequent platinum-based chemotherapy. brb-arraytools were primarily used to analyze statistically gene expression data and all other statistical analyses were performed in the r language environment (http://www.r-project.org). cluster […]


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