Statistical Microarray Analysis

[Package List] [Top]

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