Oligo package protocols

Oligo package statistics

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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
limma, methods, stats, RColorBrewer, graphics, splines, utils, R(>=2.11.0), genefilter, pd.mapping50k.xba240, oligoClasses(>=1.9.41), affyio(>=1.15.2), affxparser(>=1.17.3), Biobase(>=2.7.3), DBI(>=0.2-4), preprocessCore(>=1.9.0), hapmap100kxba, pd.hg18.60mer.expr, maqcExpression4plex
Maintained Yes

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Maintainer


  • person_outline Benilton Carvalho <>

Publication for Oligo package

Oligo package in pipelines

 (14)
2018
PMCID: 5842147
PMID: 29478844
DOI: 10.1016/j.stem.2018.01.020

[…] (https://www.bioconductor.org/packages/release/bioc/html/pdinfobuilder.html) using the platform files provided by affymetrix. the cel files were then loaded into r, rma normalized with the oligo package, and filtered to only retain probes annotated as “main” (). differential expression testing was performed using limma () and the resulting p.values were corrected […]

2017
PMCID: 5464771
PMID: 28594327
DOI: 10.7554/eLife.23190.030

[…] cel files with raw data were used and the quality control analysis was performed using arrayqualitymetrics package (). the raw data were preprocessed using the rma method available in the oligo package (). probes with no annotation were removed from analysis. finally, the resulting matrix comprised data for 53617 probes., the pca of t cell profiles was performed using the ade4 package […]

2017
PMCID: 5554239
PMID: 28801666
DOI: 10.1038/s41598-017-08010-0

[…] described, . data geo accession numbers, description of the samples, and reference to the publications are summarized in supplementary table ., the microarray raw data were imported in r, and the oligo package was used to normalize and extract the microarray expression values for the selected hassps. for each gene, the mean value for the all biological replicates was calculated to have one […]

2017
PMCID: 5713702
PMID: 29238183
DOI: 10.2147/COPD.S145445

[…] quality, signal comparability and biases, array correlation, and probe sets’ homogeneity., background correction and quantile normalization were performed for the raw array data using the oligo package (http://www.bioconductor.org/) and robust multi-array average (rma package for r). for each sample, the expression values of all probes for a given gene were reduced to a single value […]

2016
PMCID: 4839084
PMID: 27098372
DOI: 10.1186/s12931-016-0346-3

[…] model that supposes both additive and multiplicative noise components. after background correction to the individual probes, quantile normalization [] was applied, both steps are implemented in the oligo package []. normalized and corrected probes are summarized into probe sets using the median polish algorithm, which is a type of robust 2-way anova, where one factor is the array […]


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Oligo package in publications

 (46)
PMCID: 5932158
PMID: 29755398
DOI: 10.3389/fneur.2018.00266

[…] microarray affy hugene-2_0-st data (gse78115) (). specifically, we considered the 12 samples (3 replicates each) derived from 2 different cell lines ncrm-5 and inc-01 of ipsc origin. using oligo package of r bioconductor, we performed data analysis (including data normalization) to assess the differential expression pattern specific to human microglia with respect to ipscs. the oligo […]

PMCID: 5902555
PMID: 29662071
DOI: 10.1038/s41467-018-03943-0

[…] was applied on a per-chip basis for background correction. subsequent normalization across arrays, and summarization were performed using a quantile algorithm and median-polish, respectively, via oligo package from bioconductor (http://www.bioconductor.org). a differential gene expression analysis was then performed using the limma package. computed p values were corrected using the false […]

PMCID: 5938059
PMID: 29651153
DOI: 10.1038/s12276-018-0057-6

[…] and functionally overlap in the context of the interactome., expression data (gse46706) of post-mortem brain tissue from individuals aged 16–102 were downloaded, processed, and normalized using the oligo package. we implemented weighted correlation network analysis (wgcna) to identify co-expression modules reflecting aging-specific expression patterns in the brain. each module was annotated […]

PMCID: 5842147
PMID: 29478844
DOI: 10.1016/j.stem.2018.01.020

[…] (https://www.bioconductor.org/packages/release/bioc/html/pdinfobuilder.html) using the platform files provided by affymetrix. the cel files were then loaded into r, rma normalized with the oligo package, and filtered to only retain probes annotated as “main” (). differential expression testing was performed using limma () and the resulting p.values were corrected […]

PMCID: 5928615
PMID: 29512694
DOI: 10.3892/mmr.2018.8655

[…] of the gpl16686 affymetrix human gene 2.0 st array (affymetrix inc., santa clara, ca, usa) for further analysis., all the raw data were preprocessed using the robust multichip average method in the oligo package (available through bioconductor version 3.0; http://www.bioconductor.org) (). the comparison of differentially expressed lncrnas and mrnas in separate gbc tissues with normal tissues […]


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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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