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Simpleaffy specifications


Unique identifier OMICS_02034
Name Simpleaffy
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 General Public License version 2.0
Computer skills Advanced
Version 2.56.0
Stability Stable
methods, stats, graphics, BiocGenerics, Biobase, utils, grDevices, affy, genefilter, R(>=2.0.0), BiocGenerics(>=0.1.12), gcrma, affy(>=1.33.6)
Maintained Yes


No version available


Publication for Simpleaffy

Simpleaffy citations


Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus

Nat Commun
PMCID: 5916891
PMID: 29695808
DOI: 10.1038/s41467-018-03812-w

[…] Affymetrix Gene Chip microarray data underwent strict quality control processing using the “simpleaffy” package in the Bioconductor 2 suite from the R statistical programming environment. Log-scale Robust Multiarray Analysis from the “affy” package was used to normalize the data and eliminat […]


Impaired proteoglycan glycosylation, elevated TGF β signaling, and abnormal osteoblast differentiation as the basis for bone fragility in a mouse model for gerodermia osteodysplastica

PLoS Genet
PMCID: 5880397
PMID: 29561836
DOI: 10.1371/journal.pgen.1007242

[…] 1.0 microarray (Affymetrix, High Wycombe, United Kingdom). The raw image files were converted to cel files using the dChip software. The data were subjected to a quality assurance analysis using the simpleaffy package of Bioconductor. Normalization and summarization of the probe set data were conducted using the gcrma package. […]


A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification

PMCID: 5820610
PMID: 29527288
DOI: 10.5256/f1000research.11813.r24330

[…] U133A2, and U133 PLUS 2.0 gene chips; the 22,268 probe sets that are present in all platforms were included in the gene expression file. Data were MAS5.0 normalized using the justMAS function in the simpleaffy library from Bioconductor ( ) using a trimmed mean target intensity of 600 without background correction. COMBAT empirical Bayes method was used to correct for batch effects ( ). […]


In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat

PMCID: 5837750
PMID: 29545936
DOI: 10.18632/oncotarget.24370

[…] enome 230 2.0 Array. The raw .CEL files were converted to expression data using Robust Muliti-arry Average algorithm (RMA) using the Bioconductor affy package. The quality control was performed using simpleaffy package. The DEGs are identified using a t-test in the limma package and the threshold for the DEGs was set adj-pvalue < 0.05 and |logFC| > 1. […]


Integrated miRNA mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection

Sci Rep
PMCID: 5770416
PMID: 29339786
DOI: 10.1038/s41598-018-19341-x

[…] An overview of the bioinformatics pipeline is shown in Fig. . Expression data from 54 mRNA and 54 miRNA arrays were processed through discrete QC pipelines: mRNA via affyAnalysisQC and simpleaffy; miRNA via the AgiMicroRNA package. Good library quality and consistent hybridization quality were evident, however some data from both mRNA and miRNA arrays were identified as outliers and […]


A common molecular signature of intestinal type gastric carcinoma indicates processes related to gastric carcinogenesis

PMCID: 5800908
PMID: 29484116
DOI: 10.18632/oncotarget.23670

[…] Cell intensity (CEL) files storing probe-level intensity data were downloaded from NCBI’s Gene Expression Omnibus (GEO); accession numbers are described in Table . The simpleAffy Bioconductor R package was used to preprocess all raw data files. The extraction of probe level data, background correction, normalization using the robust multi-array average (RMA) algorit […]


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Simpleaffy institution(s)
Paterson Institute for Cancer Research, Manchester, UK

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