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virtualArray specifications

Information


Unique identifier OMICS_01979
Name virtualArray
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 1.8.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, plyr, graphics, BiocGenerics, Biobase, GEOquery, utils, R(>=2.15.0), affy, preprocessCore, reshape2, affydata, org.Hs.eg.db, affyPLM, gcrma, tseries, outliers, plier, lumi
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Andreas Heider

Publication for virtualArray

virtualArray citations

 (7)
library_books

Integrative multi platform meta analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers

2018
PLoS One
PMCID: 5884535
PMID: 29617451
DOI: 10.1371/journal.pone.0194844

[…] (qn) from the r package lumi []. in both cases, genes with low variability expression values were discarded to reduce false-positive rates., data from both platforms were integrated with the virtualarray software r package []. this software allows data from different microarray platforms to be merged by considering several batch effect removal and cross-platform correction methods. […]

library_books

DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated Disorders

2017
Sci Rep
PMCID: 5603607
PMID: 28924151
DOI: 10.1038/s41598-017-12084-1

[…] a specific comparison demanded two expression arrays from different platforms because the data were not present in the gse to enable comparison of the two tissues, we used the bioconductor package virtualarray, which enables the combination of raw expression data of different microarray platforms regardless of the platform and chip generation method used. the package generates a combined […]

library_books

Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo

2016
PLoS One
PMCID: 4786261
PMID: 26964064
DOI: 10.1371/journal.pone.0151335

[…] datasets generated in this study were compared with data from previous studies, deposited in public databases (ncbi gene expression omnibus, geo; ) []. r/bioconductor and the software package “virtualarray” were used to combine all data into one dataset (virtual array) [,]. the resulting new array was exported and analyzed in tm4 mev [] and archaeopteryx [], which was further used […]

library_books

Transcriptomic analysis of monocytes and macrophages derived from CLL patients which display differing abilities to respond to therapeutic antibody immune complexes

2015
Genom Data
PMCID: 4778605
PMID: 26981348
DOI: 10.1016/j.gdata.2015.11.010

[…] , . large platform specific batch effects were observed between the two datasets, so an unsupervised empirical bayes method was used to remove these batch effects after as implemented in the ‘virtualarray’ package . the two datasets were merged on common genes after multiple probes that mapped to the same gene were collapsed by taking the median expression value per sample. genes […]

library_books

Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive like pluripotency

2015
Nat Commun
PMCID: 4479042
PMID: 25968054
DOI: 10.1038/ncomms8095

[…] on our human data set and previously described mescs and episcs, and naive and primed hesc gene expression data sets (gse23402, gse15603, gse7866, gse29397, gse43421 and gse43398). we used the virtualarray r/bioconductor package to combine and normalize the different data sets, collapse by median probes targeting the same genes and identify genes present in all data sets, using gene […]

library_books

Large Scale Aggregate Microarray Analysis Reveals Three Distinct Molecular Subclasses of Human Preeclampsia

2015
PLoS One
PMCID: 4332506
PMID: 25679511
DOI: 10.1371/journal.pone.0116508

[…] in the supplied annotation files, and 8 samples with fetal growth restriction (fgr) were removed from the gse24129 data set. the individual sample sets were then aggregated into one array using the virtualarray package [] (bioconductor), which combines the compatible rows of the expression matrices and performs empirical bayes methods of normalization and batch correction for the different […]


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virtualArray institution(s)
Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, Leipzig, Germany
virtualArray funding source(s)
This work has been funded by the German Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF, PtJ-Bio: 0315883) and Vita34 AG, Leipzig.

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