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

AuthorMatthias Futschik <mfutschik@ualg.pt>
Date of publicationNone
MaintainerMatthias Futschik <mfutschik@ualg.pt>
LicenseGPL-2
Version1.52.0
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

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

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

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