affyQCReport specifications


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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affyQCReport citations

PMCID: 5135394

[…] 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 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 […]

PMCID: 3277585

[…] packages ( cel files were scrutinized for spatial artifacts by using the harshlight package [12]. classic microarray quality control report was obtained by using the affyqcreport package. expression values were obtained by using gcrma algorithm. probe-sets with standard deviation (sd) greater than 0.1 and expression values greater than 3 in at least 2 samples […]

PMCID: 3201949

[…] microarray lab [79]–[82]. this cdf included 17726 probe sets that correspond to an ncbi gene., initial quality checks of each chip were carried out using bioconductor core tools and package affyqcreport [83]. quality checks and visual inspection of array intensities showed that the quality of the array data was acceptable. robust multichip average (rma) expression values [82], [84], […]

PMCID: 2764091

[…] with personal qc and data visualization., data normalization and differential analyses were performed with the r-bioconductor statistical environment [64]. after low level diagnostics with the affyqcreport package, raw data were normalized, and log2 intensity expression summary values for each probe set was calculated using the gcrma algorithm. probe sets corresponding to control genes […]

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