arrayMagic protocols

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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

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Documentation


Publication for arrayMagic

arrayMagic in pipelines

 (2)
2008
PMCID: 2528050
PMID: 18767902
DOI: 10.1371/journal.pmed.0050184

[…] 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 […]

2006
PMCID: 3525150
PMID: 16460651
DOI: 10.1186/1479-7364-2-4-258

[…] with many packages on cran., many packages for microarray data analysis are available from cran and the bioconductor project http://www.bioconductor.org; for example, affy for affymetrix, marray and arraymagic for cdna data processing and packages for extracting signals from the scanner (spot), for gene annotation and delineating biological pathways (annotate). unlike genotype data, gene […]


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arrayMagic in publications

 (4)
PMCID: 2807430
PMID: 20035634
DOI: 10.1186/1476-4598-8-130

[…] 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 []., significance analysis of microarrays (sam) was applied to identify genes differentially regulated between normal tissue, tumor tissue gs […]

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

[…] 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 […]

PMCID: 2277374
PMID: 18248680
DOI: 10.1186/1752-0509-2-16

[…] 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 […]

PMCID: 3525150
PMID: 16460651
DOI: 10.1186/1479-7364-2-4-258

[…] with many packages on cran., many packages for microarray data analysis are available from cran and the bioconductor project http://www.bioconductor.org; for example, affy for affymetrix, marray and arraymagic for cdna data processing and packages for extracting signals from the scanner (spot), for gene annotation and delineating biological pathways (annotate). unlike genotype data, gene […]


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

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