affyPLM pipeline

affyPLM specifications

Information


Unique identifier OMICS_02017
Name affyPLM
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
Stability Stable
Maintained Yes

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Documentation


affyPLM IN pipelines

 (3)
2017
PMCID: 5493306
PMID: 28665939
DOI: 10.1371/journal.pone.0179797

[…] neuroscience institute (brainarray) at the university of michigan. array quality was assessed by computing relative log expression (rle) and normalized unscaled standard error (nuse) using the affyplm bioconductor package (version 1.34.0) [34]. moderated t tests were performed using the limma package (version 3.14.4). correction for multiple hypothesis testing was accomplished using […]

2013
PMCID: 3581155
PMID: 23484118
DOI: 10.1155/2013/458278

[…] [15], an extension for bioinformatics of the r statistical language (http://www.r-project.org/) [16]. the data quality of ten cel files obtained from the affymetrix chips were assessed with packages affyplm [17] and simple affy. on the basis of the boxplots of normalized unscaled standard errors, relative log expressions, and the clustering of between array distances (measured by median absolute […]

2012
PMCID: 3507170
PMID: 23213376
DOI: 10.1242/bio.20122238

[…] 450 and scanned on an affymetrix genechip 3000 scanner (all affymetrix, santa clara, california, usa). quality control of microarray expression data was performed using the bioconductor package affyplm (gautier et al., 2004). probe intensities from affymetrix image files (“.cel” files) were normalised using quantile normalisation (bolstad et al., 2003), and expression signals of all genes […]

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