Package: OLIN 1.91.0

Matthias Futschik

OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data

Authors:Matthias Futschik <[email protected]>

OLIN_1.91.0.tar.gz
OLIN_1.91.0.zip(r-4.7)OLIN_1.91.0.zip(r-4.6)OLIN_1.91.0.zip(r-4.5)
OLIN_1.91.0.tgz(r-4.6-any)OLIN_1.91.0.tgz(r-4.5-any)
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OLIN_1.91.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OLIN/json (API)

# Install 'OLIN' in R:

install.packages('OLIN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

sw - CDNA microarray data of SW480/SW620 experiment
sw.olin - Normalised cDNA microarray data of SW480/SW620 experiment
sw.xy - Spatial coordinates of spot locations of SW480/SW620 experiment

On BioConductor:OLIN-1.91.0(bioc 3.24)OLIN-1.90.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray twochannel qualitycontrol preprocessing visualization

4.78 score 1 packages 7 scripts 12 mentions 33 exports 5 dependencies

Last updated from:403623e48e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	138
linux-devel-x86_64	NOTE	202
source / vignettes	OK	171
linux-release-x86_64	NOTE	150
macos-release-arm64	NOTE	98
macos-oldrel-arm64	NOTE	135
windows-devel	NOTE	89
windows-release	NOTE	88
windows-oldrel	NOTE	92
wasm-release	OK	109

Exports:anovaint anovapin anovaplate anovaspatial backgroundCorrect2 bas colorbar.mxy colorbar.sig fdr.int fdr.int2 fdr.spatial fdr.spatial2 fgbg.visu ino lin m2v ma.matrix ma.vector mxy.abs.plot mxy.plot mxy2.plot oin olin p.int p.int2 p.spatial p.spatial2 sig.mask sigint.plot sigint.plot2 sigxy.plot sigxy.plot2 v2m

Dependencies:lattice limma locfit marray statmod

Introduction to OLIN

Rendered fromOLIN.Rnwusingutils::Sweave

Last update: 2022-05-06
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
One-factorial ANOVA assessing intensity-dependent bias	anovaint
One-factorial ANOVA assessing pin-dependent bias.	anovapin
One-factorial ANOVA assessing pin-dependent bias.	anovaplate
One-factorial ANOVA assessing spatial bias	anovaspatial
Background correction	backgroundCorrect2
Between-array scaling	bas
Generates a colour bar	colorbar.mxy
Generates a colour bar	colorbar.mxy.abs
Generates a colour bar for spatial significance plots	colorbar.sig
Assessment of the significance of intensity-dependent bias	fdr.int
Assessment of the significance of intensity-dependent bias	fdr.int2
Assessment of the significance of spatial bias	fdr.spatial
Assessment of the significance of spatial bias	fdr.spatial2
Visualisation of foreground and background fluorescence spot intensities in both channels	fgbg.visu
Intensity-dependent normalisation of two-colour microarrays	ino
Local intensity-dependent normalisation of two-colour microarrays	lin
Converts matrix to vector based on spot layout	m2v
Calculation of moving average for a matrix	ma.matrix
Calculation of moving average for a vector	ma.vector
Generation of MXY plots of absolute values	mxy.abs.plot
Generation of MXY plots	mxy.plot
Generation of MXY plots based on spot coordinates	mxy2.plot
Optimised intensity-dependent normalisation of two-colour microarrays	oin
Optimised local intensity-dependent normalisation of two-colour microarrays	olin
Calculates significance of intensity-dependent bias	p.int
Calculates significance of intensity-dependent bias	p.int2
Assessment of the significance of spatial bias based on p-values	p.spatial
Assessment of the significance of spatial bias based on p-values	p.spatial2
Masking of data based on significance testing	sig.mask
Visualisation of significance of intensity-dependent bias	sigint.plot
Visualisation of significance of intensity-dependent bias	sigint.plot2
Visualisation of significance tests for spatial bias	sigxy.plot
Visualisation of significance tests for spatial bias	sigxy.plot2
cDNA microarray data of SW480/SW620 experiment	sw
Normalised cDNA microarray data of SW480/SW620 experiment	sw.olin
Spatial coordinates of spot locations of SW480/SW620 experiment	sw.xy
Converts vector to matrix based on spot layout	v2m