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OLIN specifications

Information


Unique identifier OMICS_02029
Name OLIN
Alternative name Optimised Local Intensity-dependent Normalisation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.58.0
Stability Stable
Requirements
limma, methods, stats, graphics, grDevices, locfit, R(>=2.10), convert, marray
Maintained Yes

Versioning


No version available

Documentation


Publication for Optimised Local Intensity-dependent Normalisation

OLIN citations

 (11)
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Identification of biomarkers for tuberculosis susceptibility via integrated analysis of gene expression and longitudinal clinical data

2014
Front Genet
PMCID: 4109430
PMID: 25104956
DOI: 10.3389/fgene.2014.00240
call_split See protocol

[…] gene probes for 17 subjects, arranged in a loop design that included other control samples. We analyzed the two channels individually, normalized the arrays using the Bioconductor packages LIMMA and OLIN (Smyth, ; Futschik, ), and extracted the data for the samples of interest.To focus our attention on genes that would likely be associated with disease progression, we removed probes that showed i […]

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Novel cell separation method for molecular analysis of neuron astrocyte co cultures

2014
PMCID: 3906515
PMID: 24523672
DOI: 10.3389/fncel.2014.00012
call_split See protocol

[…] pression Omnibus (NCBI GEO; accession number GSE52481).Normalization of the raw data was performed, after feature extraction by Agilent software, by optimized local intensity-dependent normalization (OLIN) and optimized scaled local intensity-dependent normalization (OSLIN; ) using the R project for statistical computing (version 6.0; R project). Next, M values were scaled so that upregulated prob […]

library_books

FGF signalling through RAS/MAPK and PI3K pathways regulates cell movement and gene expression in the chicken primitive streak without affecting E cadherin expression

2011
BMC Dev Biol
PMCID: 3071786
PMID: 21418646
DOI: 10.1186/1471-213X-11-20

[…] ers much of the chicken genome. Normalization was performed according to a custom pipeline written in the R statistical computing language. Within chip normalization was performed using the R package OLIN []. Following normalization, false discovery rates were computed, and those spots demonstrating a location- or intensity-dependent bias (FDR > 1%) were subsequently masked from downstream analysi […]

library_books

Gene family structure, expression and functional analysis of HD Zip III genes in angiosperm and gymnosperm forest trees

2010
BMC Plant Biol
PMCID: 3017839
PMID: 21143995
DOI: 10.1186/1471-2229-10-273

[…] . Median foreground intensity minus median background intensity was the response variable used for the statistical analysis. Data quality was assessed using graphical analysis tools in the marray and olin packages available in Bioconductor, and by assessment of within- and between-slide Pearson product-moment correlation coefficients (r), which were calculated both from the raw intensities and aft […]

library_books

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution

2010
PLoS Genet
PMCID: 2944786
PMID: 20885784
DOI: 10.1371/journal.pgen.1001135

[…] ove background plus 1 standard deviation in both channels<60, spot pixels<40.Data normalization and filtering were performed using the Bioconductor (http://www.bioconductor.org/) packages marray and OLIN as well as custom scripts. OLIN was used for intra-slide normalization and log2 transformation.For statistical analysis of meiotic time course data, data from a given probe were included only i […]

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Comparison and consolidation of microarray data sets of human tissue expression

2010
BMC Genomics
PMCID: 2885367
PMID: 20465848
DOI: 10.1186/1471-2164-11-305
call_split See protocol

[…] cDNA microarrays containing 39,711 human cDNAs. The raw data was downloaded from the Stanford Microarray Database. We normalized the raw data using optimized local intensity-dependent normalization (OLIN) which is based on iterative local regression and optimization of model parameters by internal cross-validation. It has been demonstrated that it can correct favourably for potential dye and spat […]

Citations

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OLIN institution(s)
Institute for Theoretical Biology, Humboldt-Universität, Berlin, Germany

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