# Optimized local intensity-dependent normalisation of two-color microarrays

## Documentation for package ‘OLIN’ version 1.24.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help 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 intensities in both channels
ino | Intensity-dependent normalisation of two-colour microarrays
lin | Local intensity-dependent normalisation of two-colour microarrays
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
mxy.abs.plot | Generation of MXY plots of absolute values
mxy.plot | Generation of MXY plots
mxy2.plot | Generation of MXY plots based on spot coordinates
oin | Optimised intensity-dependent normalisation of two-colour microarrays
olin | Optimised local intensity-dependent normalisation of two-colour microarrays
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-values
p.spatial2 | Assessment of the significance of spatial bias based on p-values
sig.mask | Masking of data based on significance testing
sigint.plot | Visualisation of significance of intensity-dependent bias
sigint.plot2 | Visualisation of significance of intensity-dependent bias
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 experiment
v2m | Converts vector to matrix based on spot layout