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

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

Author
Matthias Futschik <mfutschik@ualg.pt>
Date of publication
None
Maintainer
Matthias Futschik <mfutschik@ualg.pt>
License
GPL-2
Version
1.52.0
URLs

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

Files in this package

OLIN/DESCRIPTION
OLIN/NAMESPACE
OLIN/R
OLIN/R/anovaint.R
OLIN/R/anovapin.R
OLIN/R/anovaplate.R
OLIN/R/anovaspatial.R
OLIN/R/backgroundCorrect2.R
OLIN/R/bas.R
OLIN/R/colorbar.mxy.R
OLIN/R/colorbar.mxy.abs.R
OLIN/R/colorbar.sig.R
OLIN/R/fdr.int.R
OLIN/R/fdr.int2.R
OLIN/R/fdr.spatial.R
OLIN/R/fdr.spatial2.R
OLIN/R/fgbg.visu.R
OLIN/R/ino.R
OLIN/R/lin.R
OLIN/R/m2v.R
OLIN/R/ma.matrix.R
OLIN/R/ma.vector.R
OLIN/R/mxy.abs.plot.R
OLIN/R/mxy.plot.R
OLIN/R/mxy2.plot.R
OLIN/R/oin.R
OLIN/R/olin.R
OLIN/R/p.int.R
OLIN/R/p.int2.R
OLIN/R/p.spatial.R
OLIN/R/p.spatial2.R
OLIN/R/sig.mask.R
OLIN/R/sigint.plot.R
OLIN/R/sigint.plot2.R
OLIN/R/sigxy.plot.R
OLIN/R/sigxy.plot2.R
OLIN/R/v2m.R
OLIN/build
OLIN/build/vignette.rds
OLIN/data
OLIN/data/sw.RData
OLIN/data/sw.olin.RData
OLIN/data/sw.xy.RData
OLIN/inst
OLIN/inst/CITATION
OLIN/inst/doc
OLIN/inst/doc/OLIN.R
OLIN/inst/doc/OLIN.Rnw
OLIN/inst/doc/OLIN.pdf
OLIN/inst/scripts
OLIN/inst/scripts/OLIN.tex
OLIN/inst/scripts/scatter.png
OLIN/man
OLIN/man/anovaint.Rd
OLIN/man/anovapin.Rd
OLIN/man/anovaplate.Rd
OLIN/man/anovaspatial.Rd
OLIN/man/backgroundCorrect2.Rd
OLIN/man/bas.Rd
OLIN/man/colorbar.mxy.Rd
OLIN/man/colorbar.mxy.abs.Rd
OLIN/man/colorbar.sig.Rd
OLIN/man/fdr.int.Rd
OLIN/man/fdr.int2.Rd
OLIN/man/fdr.spatial.Rd
OLIN/man/fdr.spatial2.Rd
OLIN/man/fgbg.visu.Rd
OLIN/man/ino.Rd
OLIN/man/lin.Rd
OLIN/man/m2v.Rd
OLIN/man/ma.matrix.Rd
OLIN/man/ma.vector.Rd
OLIN/man/mxy.abs.plot.Rd
OLIN/man/mxy.plot.Rd
OLIN/man/mxy2.plot.Rd
OLIN/man/oin.Rd
OLIN/man/olin.Rd
OLIN/man/p.int.Rd
OLIN/man/p.int2.Rd
OLIN/man/p.spatial.Rd
OLIN/man/p.spatial2.Rd
OLIN/man/sig.mask.Rd
OLIN/man/sigint.plot.Rd
OLIN/man/sigint.plot2.Rd
OLIN/man/sigxy.plot.Rd
OLIN/man/sigxy.plot2.Rd
OLIN/man/sw.Rd
OLIN/man/sw.olin.Rd
OLIN/man/sw.xy.Rd
OLIN/man/v2m.Rd
OLIN/vignettes
OLIN/vignettes/OLIN.Rnw
OLIN/vignettes/scatter.png