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 citations

 (5)
2017
PMCID: 5581396

[…] using r, the bioconductor (gentleman et al., 2004), and a robust multi-chip average (rma) (bolstad et al., 2003; irizarry et al., 2003). the quality of the genechip data was assessed using the affyplm package (bolstad et al., 2005). the annotation of each gene in the csv file ath1-121501.na31.annot.csv (downloaded in april 2012)6 released by affymetrix was used. for stress treatment- […]

2013
PMCID: 3581155

[…] [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

[…] 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 […]

2010
PMCID: 3161387

[…] inc.), quality assessment of the arrays was performed with the tools available in the gene chip operating software, version 1.4 (affymetrix, inc.) and the bioconductor packages affyqcreport [16] and affyplm [17], r version 2.8, bioconductor version 2.3 [18]. the microarray data has been assigned series number gse16149 in the gene expression omnibus (geo, http://www.ncbi.nlm.nih.gov/geo/)., array […]

2008
PMCID: 2528050

[…] 11). there are many comprehensive, free, and open-source packages in bioconductor [53] for quality assessment including arraymagic [54] for the two-color technology platform and simpleaffy [55], and affyplm [56] for the affymetrix platform., next, all good quality arrays should be preprocessed consistently to remove any systematic differences (step 12). this is an important stage, since […]

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