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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OLIN")
AuthorMatthias Futschik <mfutschik@ualg.pt>
Bioconductor views Microarray Preprocessing QualityControl TwoChannel Visualization
Date of publicationNone
MaintainerMatthias Futschik <mfutschik@ualg.pt>
LicenseGPL-2
Version1.54.0
http://olin.sysbiolab.eu

View on Bioconductor

Man pages

anovaint: One-factorial ANOVA assessing intensity-dependent bias

anovapin: One-factorial ANOVA assessing pin-dependent bias.

anovaplate: One-factorial ANOVA assessing pin-dependent bias.

anovaspatial: One-factorial ANOVA assessing spatial bias

backgroundCorrect2: Background correction

bas: Between-array scaling

colorbar.mxy: Generates a colour bar

colorbar.mxy.abs: Generates a colour bar

colorbar.sig: Generates a colour bar for spatial significance plots

fdr.int: Assessment of the significance of intensity-dependent bias

fdr.int2: Assessment of the significance of intensity-dependent bias

fdr.spatial: Assessment of the significance of spatial bias

fdr.spatial2: Assessment of the significance of spatial bias

fgbg.visu: Visualisation of foreground and background fluorescence spot...

ino: Intensity-dependent normalisation of two-colour microarrays

lin: Local intensity-dependent normalisation of two-colour...

m2v: Converts matrix to vector based on spot layout

ma.matrix: Calculation of moving average for a matrix

ma.vector: Calculation of moving average for a vector

mxy2.plot: Generation of MXY plots based on spot coordinates

mxy.abs.plot: Generation of MXY plots of absolute values

mxy.plot: Generation of MXY plots

oin: Optimised intensity-dependent normalisation of two-colour...

olin: Optimised local intensity-dependent normalisation of...

p.int: Calculates significance of intensity-dependent bias

p.int2: Calculates significance of intensity-dependent bias

p.spatial: Assessment of the significance of spatial bias based on...

p.spatial2: Assessment of the significance of spatial bias based on...

sigint.plot: Visualisation of significance of intensity-dependent bias

sigint.plot2: Visualisation of significance of intensity-dependent bias

sig.mask: Masking of data based on significance testing

sigxy.plot: Visualisation of significance tests for spatial bias

sigxy.plot2: Visualisation of significance tests for spatial bias

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...

v2m: Converts vector to matrix based on spot layout

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.