affyQCReport protocols

affyQCReport specifications

Information


Unique identifier OMICS_02018
Name affyQCReport
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


affyQCReport IN pipelines

 (3)
2016
PMCID: 5054603
PMID: 27774052
DOI: 10.3389/fncel.2016.00230

[…] statistical and data mining works were performed in r-environment (r core team, 2016) with bioconductor packages (huber et al., 2015). quality assessment of microarrays (n = 12) was performed using affyqcreport (kauffmann et al., 2009). for quality control data regarding rna integrity, see supplementary figure 3. raw microarray data were pre-processed for analysis using rma (robust multi-array […]

2016
PMCID: 5135394
PMID: 27848912
DOI: 10.7554/eLife.20542.028

[…] et al., 2010). all data processing was done using the statistics package r (version 2.6.2, rrid:scr_001905) that is freely available at http://www.rproject.org/. quality control was done using the affyqcreport package in r (rrid:scr_001318). in addition, coefficients of variation (cv) were calculated between replicates as a quantitative measure of data quality and consistency […]

2014
PMCID: 4096512
PMID: 25020062
DOI: 10.1371/journal.pone.0102359

[…] arrays pre-processing and analysis were performed using r and the bioconductor package (http://www.bioconductor.org/) and passed through array quality control using the affyqcreport tool. raw intensities were normalized using rma and scaled to a 2% trimmed mean of 150. probes with normalized expression values below 50 in both groups were filtered out. differential […]

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