Oligo package pipeline

Oligo package specifications


Unique identifier OMICS_14343
Name Oligo package
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format CEL, XYS
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements oligoClasses
Maintained Yes



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  • person_outline Benilton Carvalho <>

Publication for Oligo package

Oligo package citations

PMCID: 5506428

[…] scanner 3000 7g (affymetrix, canada). two replicates were performed for each sample. gene expression data from affymetrix hugene 2.0 microarrays were normalized using the rma function of the r oligo package. quality analysis of the microarrays was performed using the r arrayqualitymetrics package. fold change and significance for transcript cluster identifiers between conditions […]

PMCID: 5407452

[…] on the affymetrix genechip 3000s scanner as per the manufacturer’s instructions., after passing quality control, cel files were normalised using the robust multi-array average (rma) algorithm (oligo package in r, version 1.38.0). adjustments for batch effects was performed using combat (sva package, version 3.22.0) ( leek et al., 2012). one adrenal sample that was an extreme outlier […]

PMCID: 5464771

[…] raw data were used and the quality control analysis was performed using arrayqualitymetrics package (kauffmann et al., 2009). the raw data were preprocessed using the rma method available in the oligo package (carvalho and irizarry, 2010). probes with no annotation were removed from analysis. finally, the resulting matrix comprised data for 53617 probes., the pca of t cell profiles […]

Oligo package institution(s)
Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
Oligo package funding source(s)
Doctoral scholarship awarded by the Brazilian Funding Agency CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) and National Institutes of Health grants R01RR021967 and P41HG004059.

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