# Statistical Microarray Analysis

## -- C --

 c.func Internal sma functions c.min Internal sma functions chen.func.rotate Internal sma functions chen.plot.rotate Internal sma functions chen.poly Internal sma functions chur.em.func Internal sma functions chur.M.to.e.func Internal sma functions chur.norm.func Internal sma functions chur.pdf Internal sma functions chur.wrapper.func Internal sma functions cl Internal sma functions cor.na Basic Statistical Functions for Handling Missing Values

## -- D --

 dc.min Internal sma functions draw.image.func Spatial Representation of Microarray Spot Statistics

## -- F --

 func.em Internal sma functions

## -- G --

 givelim Internal sma functions

## -- I --

 id2image Converting an id tag to a Set of Image Coordinates and Vice Versa image2id Converting an id tag to a Set of Image Coordinates and Vice Versa in.func Internal sma functions init.addinfo Adding Information to a Data Structure for Multi-slide Microarray Experiments init.ctl.index Generates co-ordinates of spots. init.data Creating a Data Structure for Multi-slide Microarray Experiments init.grid Initialization of Grid Parameters init.name.exp Set and Read the Names of Experimental Data. init.read.exp Reads the Output of the Computed Statistics init.show.exp Set and Read the Names of Experimental Data. is.even Determining if a Value is Odd or Even is.odd Determining if a Value is Odd or Even

## -- L --

 length.na Basic Statistical Functions for Handling Missing Values lf.func Internal sma functions lod2 Internal sma functions lods.func Internal sma functions log.na Basic Statistical Functions for Handling Missing Values ls.variance Internal sma functions

## -- M --

 ma.func Calculation of log Intensity Ratios and Average log Intensities mean.na Basic Statistical Functions for Handling Missing Values mouse.data Internal sma functions mouse.gnames Mouse Gene Expression Data from cDNA microarray mouse.lratio Internal sma functions mouse.setup Internal sma functions mouse.t2 Internal sma functions mouse1 Mouse Gene Expression Data from cDNA microarray mouse2 Mouse Gene Expression Data from cDNA microarray mouse3 Mouse Gene Expression Data from cDNA microarray mouse4 Mouse Gene Expression Data from cDNA microarray mouse5 Mouse Gene Expression Data from cDNA microarray mouse6 Mouse Gene Expression Data from cDNA microarray MouseArray Mouse Gene Expression Data from cDNA microarray

## -- O --

 order.na Basic Statistical Functions for Handling Missing Values

## -- P --

 plot.bayesian Plots lodscore vs effect estimate (the output of stat.bayesian() or stat.bay.est()). plot.confband.lines Adding Lines Satisfying a Confidence Criterion to the Current M vs A Plot plot.confband.points Highlights a Set of Points on the Current M vs A Plot plot.confband.text Add Selected Text to an M vs A Plot plot.cor Red and Green Color Image of Correlation Matrix plot.mat Red and Green Color Image of Data Matrix plot.mva M vs. A Plot plot.print.tip.lowess M vs. A Plot with print tip lowess lines plot.qq Histogram and Normal Quantile-Quantile plot plot.qqline Add Line Going Through the Quantiles of a Q-Q Plot plot.scale.box Box plots for microarray plot.single.slide M vs. A Plot plot.smooth.line Adding Lowess Lines to Current Plot plot.spatial Spatial Representation of Microarray Spot Statistics plot.svb Plot of Signal vs. Background plot.t2 Diagnostic Plots for Two-Sample t-statistics prod.na Basic Statistical Functions for Handling Missing Values

## -- Q --

 quantile.na Basic Statistical Functions for Handling Missing Values

## -- R --

 read.genepix Reading in Data Generated by the Image Analysis Package GenePix. read.spot Reading in Data Generated by the Image Analysis Package Spot rgcolors.func Red and Green Color Specification

## -- S --

 scale.na Basic Statistical Functions for Handling Missing Values setup.bayesian Internal sma functions spatial.func Spatial Representation of Microarray Spot Statistics sq.func Internal sma functions sq2.func Internal sma functions stat.bay.est Calculates an Odds Ratio for Each Gene in a Multi-slide Microarray Experiment. stat.bayesian Calculates an Odds Ratio of Each Gene in a Multi-slide microarray Experiment stat.bwss Between and Within Group Sum of Squares Calculation stat.Chen Apply Chen's single slide method stat.Chen.ma Internal sma functions stat.ChurSap Apply Sapir and Churchills single slide method stat.ChurSap.ma Internal sma functions stat.diag.da Diagonal Discriminant Analysis stat.gnames Sort Genes According to the Value of a Statistic stat.ma Calculation of log Intensity Ratios and Average log Intensities stat.Newton Apply Newtons single slide method stat.Newton.ma Internal sma functions stat.norm.exp Normalization of log Intensity Ratios across slides / experiments. stat.t2 Two-sample t-statistics sum.na Basic Statistical Functions for Handling Missing Values svb.func Plot of Signal vs. Background

## -- T --

 t2stat.func Two-sample t-statistics

## -- V --

 va.func Internal sma functions va2.func Internal sma functions var.na Basic Statistical Functions for Handling Missing Values

## -- W --

 write.spot Writing in Data Generated by the Image Analysis Package Spot