Optimized local intensity-dependent normalisation of two-color microarrays


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Documentation for package ‘OLIN’ version 1.28.0

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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 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
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