Package: OLIN 1.83.0

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]>

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OLIN.pdf |OLIN.html✨
OLIN/json (API)

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

Peer review:

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-1.83.0(bioc 3.20)OLIN-1.82.0(bioc 3.19)

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

microarraytwochannelqualitycontrolpreprocessingvisualization

33 exports 4.78 score 5 dependencies 1 dependents 12 mentions 2 scripts 236 downloads

Last updated 5 months agofrom:a968b1b34f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winNOTESep 18 2024
R-4.5-linuxNOTESep 18 2024
R-4.4-winNOTESep 18 2024
R-4.4-macNOTESep 18 2024
R-4.3-winNOTESep 18 2024
R-4.3-macNOTESep 18 2024

Exports:anovaintanovapinanovaplateanovaspatialbackgroundCorrect2bascolorbar.mxycolorbar.sigfdr.intfdr.int2fdr.spatialfdr.spatial2fgbg.visuinolinm2vma.matrixma.vectormxy.abs.plotmxy.plotmxy2.plotoinolinp.intp.int2p.spatialp.spatial2sig.masksigint.plotsigint.plot2sigxy.plotsigxy.plot2v2m

Dependencies:latticelimmalocfitmarraystatmod

Introduction to OLIN

Rendered fromOLIN.Rnwusingutils::Sweaveon Sep 18 2024.

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

Readme and manuals

Help Manual

Help pageTopics
One-factorial ANOVA assessing intensity-dependent biasanovaint
One-factorial ANOVA assessing pin-dependent bias.anovapin
One-factorial ANOVA assessing pin-dependent bias.anovaplate
One-factorial ANOVA assessing spatial biasanovaspatial
Background correctionbackgroundCorrect2
Between-array scalingbas
Generates a colour barcolorbar.mxy
Generates a colour barcolorbar.mxy.abs
Generates a colour bar for spatial significance plotscolorbar.sig
Assessment of the significance of intensity-dependent biasfdr.int
Assessment of the significance of intensity-dependent biasfdr.int2
Assessment of the significance of spatial biasfdr.spatial
Assessment of the significance of spatial biasfdr.spatial2
Visualisation of foreground and background fluorescence spot intensities in both channelsfgbg.visu
Intensity-dependent normalisation of two-colour microarraysino
Local intensity-dependent normalisation of two-colour microarrayslin
Converts matrix to vector based on spot layoutm2v
Calculation of moving average for a matrixma.matrix
Calculation of moving average for a vectorma.vector
Generation of MXY plots of absolute valuesmxy.abs.plot
Generation of MXY plotsmxy.plot
Generation of MXY plots based on spot coordinatesmxy2.plot
Optimised intensity-dependent normalisation of two-colour microarraysoin
Optimised local intensity-dependent normalisation of two-colour microarraysolin
Calculates significance of intensity-dependent biasp.int
Calculates significance of intensity-dependent biasp.int2
Assessment of the significance of spatial bias based on p-valuesp.spatial
Assessment of the significance of spatial bias based on p-valuesp.spatial2
Masking of data based on significance testingsig.mask
Visualisation of significance of intensity-dependent biassigint.plot
Visualisation of significance of intensity-dependent biassigint.plot2
Visualisation of significance tests for spatial biassigxy.plot
Visualisation of significance tests for spatial biassigxy.plot2
cDNA microarray data of SW480/SW620 experimentsw
Normalised cDNA microarray data of SW480/SW620 experimentsw.olin
Spatial coordinates of spot locations of SW480/SW620 experimentsw.xy
Converts vector to matrix based on spot layoutv2m