Oligo package protocols

Oligo package specifications

Information


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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Maintainer


  • person_outline Benilton Carvalho <>

Publication for Oligo package

Oligo package IN pipelines

 (4)
2017
PMCID: 5506428
PMID: 28597562
DOI: 10.1111/acel.12621

[…] 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 […]

2014
PMCID: 4115254
PMID: 24477640
DOI: 10.1093/jxb/ert489

[…] bioconductor tools (gentleman et al., 2004). after quality control with the arrayqualitymetrics package (kauffmann et al., 2009), expression intensities were normalized with rma function with the oligo package (carvalho and irizarry, 2010). genes differentially expressed between high and low glucose concentration in the culture media were identified using the moderate t-test in the limma […]

2013
PMCID: 3795667
PMID: 24146813
DOI: 10.1371/journal.pone.0076051

[…] redwood city, ca)., analysis of the affymetrix rat gene 1.1 st arrays was performed using r/bioconductor [33]. the microarrays were normalized with the robust multi-array average (rma) algorithm (oligo package version 1.22.0) [39]. the intensity of the genomic probes below the median intensity of antigenomic probes (considered as a background value) were corrected to this median value. probes […]

2012
PMCID: 3436881
PMID: 22970192
DOI: 10.1371/journal.pone.0044267

[…] expression omnibus accession number gse31019)., data analysis was performed using bioconductor 2.6 [66] in r 2.11.0. the data from 3 independent biological replicates were preprocessed using the oligo package 1.12.2 [67] with the rma algorithm [68]. statistically significant changes in gene expression between treatment and control groups were determined using the empirical bayes moderated […]

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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