# Statistical Microarray Analysis

## Documentation for package `sma' version 0.5.14

## Help Pages

C D F G I L M N O P Q R S T V W

## -- 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

## -- N --

newton.plot.rotate | Internal sma functions
norm.l.func | Calculation of log Intensity Ratios and Average log Intensities
norm.pin.func | Calculation of log Intensity Ratios and Average log Intensities
norm.scale.func | Calculation of log Intensity Ratios and Average log Intensities
nploglik | Internal sma functions
nploglikderiv | Internal sma functions

## -- 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