Simpleaffy protocols

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Simpleaffy specifications

Information


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
Requirements
methods, stats, graphics, BiocGenerics, Biobase, utils, grDevices, affy, genefilter, R(>=2.0.0), BiocGenerics(>=0.1.12), gcrma, affy(>=1.33.6)
Maintained Yes

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Publication for Simpleaffy

Simpleaffy in pipelines

 (22)
2018
PMCID: 5916891
PMID: 29695808
DOI: 10.1038/s41467-018-03812-w

[…] were induced for focal ischemic brain injury through middle cerebral artery occlusion as described., 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 […]

2017
PMCID: 5500850
PMID: 28671182
DOI: 10.1038/ncomms15932

[…] the custom software (2011–2012). r/bioconductor packages were utilized for bioinformatics analyses: biobase (v. 2.30.0), biocgenerics (v. 0.16.1), aroma.affymetrix (v. 1.2.0), limma (v. 3.26.9), simpleaffy (v. 2.46.0), affy (v. 1.48.0), topgo (v. 2.12.0) and go.db (v. 2.9.0). microsoft excel (various versions) was used for browsing and editing of tables., code for r/bioconductor packages […]

2017
PMCID: 5647037
PMID: 28791394
DOI: 10.3892/mmr.2017.7158

[…] was used for raw microarray data preprocessing, including concluding quality assessment (qa), quality control (qc), background correction and normalization. the r packages using for qa/qc were simpleaffy (), affyplm and arrayqualitymetrics (). through qc checks, the sample gsm312887 within the dataset was disqualified () and excluded from subsequent analysis. robust multi-array average […]

2017
PMCID: 5739103
PMID: 28742980
DOI: 10.1080/15592294.2017.1356555

[…] (genechip hybridization, wash & stain kit, affymetrix, #900720), arrays were scanned (affymetrix genechip scanner 3000, affymetrix)., analysis of the raw expression data was performed using the simpleaffy and the affy r packages for uploading and rma normalization of the data. the lmfit, contrasts.fit, as well as the ebayes functions of the limma package were used to preprocess the data, […]

2016
PMCID: 5031250
PMID: 27654331
DOI: 10.1186/s12864-016-2851-7

[…] [] were used to generate images, histograms, box plots, degradation plots, ma plots and scatter plots to evaluate the quality of the hybridized arrays. the arrays were read in using functions from simpleaffy []. the data were pre-processed and normalised using the factor analysis for robust microarray summarisation (farms) algorithm []. the data were normalised using the quantile normalisation […]


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Simpleaffy in publications

 (137)
PMCID: 5916891
PMID: 29695808
DOI: 10.1038/s41467-018-03812-w

[…] were induced for focal ischemic brain injury through middle cerebral artery occlusion as described., 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 […]

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., for library preparation the truseq rna sample prep kit was used […]

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 ( )., gene […]

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

[…] 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., gsea is a computational method […]

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

[…] and to prepare graphs., 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) […]


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

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