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arrayMagic specifications

Information


Unique identifier OMICS_00743
Name arrayMagic
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for arrayMagic

arrayMagic citations

 (8)
library_books

caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts

2011
BMC Bioinformatics
PMCID: 3230913
PMID: 21957981
DOI: 10.1186/1471-2105-12-383

[…]  [] addresses these deficiencies and seeks to replace or augment existing methods to improve the reproducibility of microarray experimentation.Quality Assurance (QA) tools, such as SmudgeMiner [] and arrayMagic [] provide intuitive images of damaged arrays through the use of heat maps, but they do not provide correction methods for observed errors. In fact, RMA and dChip also readily provide simil […]

library_books

Differential expression of apoptotic genes PDIA3 and MAP3K5 distinguishes between low and high risk prostate cancer

2009
Mol Cancer
PMCID: 2807430
PMID: 20035634
DOI: 10.1186/1476-4598-8-130

[…] s. Data were analyzed using the GenePix 4.0 software (Axon Instruments, Foster City, USA). Low quality measurements were excluded from further analysis. Raw expression values were pre-processed using ArrayMagic [] and thereby normalized using the VSN method []. […]

library_books

GATA factors in human neuroblastoma: distinctive expression patterns in clinical subtypes

2009
Br J Cancer
PMCID: 2768442
PMID: 19707195
DOI: 10.1038/sj.bjc.6605276

[…] e colour Cy-labelled reference cRNA to a customised 11 kb oligonucleotide-microarray (Agilent Technologies, Waldbronn, Germany). Quality control of raw data was carried out using the software package arrayMagic (). After normalisation of the expression profiles using the variance stabilisation algorithm (), data from dye-flipped chip pairs were averaged to yield one intensity value for every gene […]

library_books

Independent evolution of neurotoxin and flagellar genetic loci in proteolytic Clostridium botulinum

2009
BMC Genomics
PMCID: 2674064
PMID: 19298644
DOI: 10.1186/1471-2164-10-115

[…] enePix 4000B microarray laser scanner (Axon Instruments, CA, USA). The data from detected features was initially processed using the GenePix Pro v.6.0 software supplied with the scanner.The R package arrayMagic v.1.14.0 [] was used to assess the quality of the hybridisations by generating a diagnostic plot showing the pairwise similarities between all hybridisations. The pairwise similarity score […]

library_books

Key Issues in Conducting a Meta Analysis of Gene Expression Microarray Datasets

2008
PLoS Med
PMCID: 2528050
PMID: 18767902
DOI: 10.1371/journal.pmed.0050184

[…] e may wish to first identify and remove any arrays that are of poor quality (Step 11). There are many comprehensive, free, and open-source packages in BioConductor [] for quality assessment including arrayMagic [] for the two-color technology platform and Simpleaffy [], and affyPLM [] for the Affymetrix platform.Next, all good quality arrays should be preprocessed consistently to remove any system […]

library_books

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

2008
BMC Syst Biol
PMCID: 2277374
PMID: 18248680
DOI: 10.1186/1752-0509-2-16

[…] sing the limma (v.2.10.5) Bioconductor open access package run in the R statistical framework (R Development Core Team, 2005). Quality of the hybridization was assessed with the Bioconductor packages arrayMagic v.1.14.0 and arrayQuality v.1.12.0. Log-fold (M) over variance (A) plots (M-A plots) were used to determine the most appropriate background correction method. We used basic subtraction in t […]

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arrayMagic institution(s)
Department of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany

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