affy - analysis of Affymetrix GeneChip data at the probe level

By Laurent Gautier, Leslie M. Cope, Benjamin M. Bolstad, Rafael A. Irizarry. Bioinform., 2004

5,313 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/13e6d58e6006bed58b0b67263ef94b3ac4c13293

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Citations in the corpus

Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures (2019, methodology): “The raw data for the dataset from Affymetrix were processed using the RMA algorithm for background adjustment in the Affy software package (23).”
Transcriptomic Footprints Disclose Specificity of Reactive Oxygen Species Signaling in Arabidopsis1[W] (2006, methodology): “For Affymetrix ATH1 data sets, the raw data (CEL files) were collectively processed by Robust Multiarray Average (gcRMA; Bolstad et al., 2003; Irizarry et al., 2003a, 2003b) using the affy package of R/Bioconductor (Gautier et al., 2004).”
Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients (2014, positive): “Normalization was performed independently on each cohort using R version 3.01, Bioconductor Affy Package 1.38.1, Robust Multichip Average (Gautier et al , 2004), and ComBat (Johnson et al , 2007) was applied for batch adjustment on the compiled, normalized data sets separately.”
Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients. (2012, methodology): “CEL files were MAS5 normalized in the R statistical environment (www.r-project.org) using the affy Bioconductor library (Gautier et al. 2004).”
Regional and cellular gene expression changes in human Huntington's disease brain. (2006, methodology): “Gene expression was quantified by robust multi-array analysis (44,45) using the affy package (46).”
Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsisw⃞ (2005, methodology): “All GeneChip arrays were processed first by robust multiarray average (RMA) (Irizarry et al., 2003) using the R package affy (Gautier et al., 2004).”
Network-based inference of protein activity helps functionalize the genetic landscape of cancer (2016, methodology): “The Affymetrix platform datasets were summarized by MAS5 (affy R-package 50,51 ) using probe-clusters generated by the “cleaner” algorithm 52 .”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, methodology): “The above processing was implemented using the affy package of the R Bioconductor software (28).”
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models (2017, methodology): “GSE35144 28 , GSE64392 16 , GSE74843 15 and E-MTAB-991 14 PDX/organoid microarray gene expression datasets were downloaded from GEO 49 /ArrayExpress 50 and CEL files were pre-processed using the justRMA function in the R package affy 51 , with brainarray Entrez v20 CDFs 52 .”
GENT2: an updated gene expression database for normal and tumor tissues (2019, methodology): “We collected data from the NCBI GEO public database and processed them with the MAS5 algorithm using the affy package in Bioconductor [7].”
An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients (2010, methodology): “r-project.org) using the affy Bioconductor library [ 13 ].”