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OLIN (version 1.50.0)

Optimized local intensity-dependent normalisation of two-color microarrays

Description

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

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Version

Version

1.50.0

License

GPL-2

Maintainer

Matthias Futschik

Last Published

February 15th, 2017

Functions in OLIN (1.50.0)

mxy.abs.plot

Generation of MXY plots of absolute values
sigxy.plot

Visualisation of significance tests for spatial bias
lin

Local intensity-dependent normalisation of two-colour microarrays
colorbar.mxy

Generates a colour bar
ma.matrix

Calculation of moving average for a matrix
ma.vector

Calculation of moving average for a vector
sigxy.plot2

Visualisation of significance tests for spatial bias
p.int

Calculates significance of intensity-dependent bias
p.spatial2

Assessment of the significance of spatial bias based on p-values
sw.olin

Normalised cDNA microarray data of SW480/SW620 experiment
sigint.plot2

Visualisation of significance of intensity-dependent bias
p.int2

Calculates significance of intensity-dependent bias
sigint.plot

Visualisation of significance of intensity-dependent bias
fgbg.visu

Visualisation of foreground and background fluorescence spot intensities in both channels
colorbar.mxy.abs

Generates a colour bar
ino

Intensity-dependent normalisation of two-colour microarrays
sw.xy

Spatial coordinates of spot locations of SW480/SW620 experiment
backgroundCorrect2

Background correction
sw

cDNA microarray data of SW480/SW620 experiment
p.spatial

Assessment of the significance of spatial bias based on p-values
m2v

Converts matrix to vector based on spot layout
anovaspatial

One-factorial ANOVA assessing spatial bias
mxy2.plot

Generation of MXY plots based on spot coordinates
fdr.int2

Assessment of the significance of intensity-dependent bias
OLINgui

Graphical user interface for OLIN package
anovapin

One-factorial ANOVA assessing pin-dependent bias.
anovaint

One-factorial ANOVA assessing intensity-dependent bias
oin

Optimised intensity-dependent normalisation of two-colour microarrays
sig.mask

Masking of data based on significance testing
v2m

Converts vector to matrix based on spot layout
fdr.int

Assessment of the significance of intensity-dependent bias
olin

Optimised local intensity-dependent normalisation of two-colour microarrays
mxy.plot

Generation of MXY plots
colorbar.sig

Generates a colour bar for spatial significance plots
anovaplate

One-factorial ANOVA assessing pin-dependent bias.
fdr.spatial

Assessment of the significance of spatial bias
fdr.spatial2

Assessment of the significance of spatial bias
bas

Between-array scaling