Entry: id2image
Aliases: id2image image2id
Keywords: attribute image, id
Description: Converting an id tag to a Set of Image Coordinates and Vice Versa
URL: ../../../library/sma/html/id2image.html

Entry: init.addinfo
Aliases: init.addinfo
Keywords: microarray, quality information. manip
Description: Adding Information to a Data Structure for Multi-slide Microarray Experiments
URL: ../../../library/sma/html/init.addinfo.html

Entry: init.ctl.index
Aliases: init.ctl.index
Keywords: 
Description: Generates co-ordinates of spots.
URL: ../../../library/sma/html/init.ctl.index.html

Entry: init.data
Aliases: init.data
Keywords: attribute microarray.
Description: Creating a Data Structure for Multi-slide Microarray Experiments
URL: ../../../library/sma/html/init.data.html

Entry: init.grid
Aliases: init.grid
Keywords: misc microarray, grid.
Description: Initialization of Grid Parameters
URL: ../../../library/sma/html/init.grid.html

Entry: init.names
Aliases: init.name.exp init.show.exp
Keywords: attribute filename
Description: Set and Read the Names of Experimental Data.
URL: ../../../library/sma/html/init.names.html

Entry: init.read.exp
Aliases: init.read.exp
Keywords: file
Description: Reads the Output of the Computed Statistics
URL: ../../../library/sma/html/init.read.exp.html

Entry: is.odd
Aliases: is.odd is.even
Keywords: logic
Description: Determining if a Value is Odd or Even 
URL: ../../../library/sma/html/is.odd.html

Entry: MouseArray
Aliases: mouse1 mouse2 mouse3 mouse4 mouse5 mouse6 mouse.gnames
Keywords: datasets
Description: Mouse Gene Expression Data from cDNA microarray
URL: ../../../library/sma/html/MouseArray.html

Entry: na
Aliases: log.na sum.na mean.na var.na cor.na quantile.na length.na order.na scale.na prod.na
Keywords: 
Description: Basic Statistical Functions for Handling Missing Values
URL: ../../../library/sma/html/na.html

Entry: plot.bayesian
Aliases: plot.bayesian
Keywords: hplot microarray, bayesian, lodsratio
Description: Plots an Odds Ratio of Each Gene in a Multi-slide microarray Experiment
URL: ../../../library/sma/html/plot.bayesian.html

Entry: plot.confband.lines
Aliases: plot.confband.lines
Keywords: microarray, point-wise confidence band. aplot
Description: Adding Lines Satisfying a Confidence Criterion to the Current M   vs A Plot
URL: ../../../library/sma/html/plot.confband.lines.html

Entry: plot.confband.points
Aliases: plot.confband.points
Keywords: aplot microarray, point-wise confidence band.
Description: Highlights a Set of Points on the Current M vs A Plot
URL: ../../../library/sma/html/plot.confband.points.html

Entry: plot.confband.text
Aliases: plot.confband.text
Keywords: aplot microarray, point-wise confidence band.
Description: Add Selected Text to an M vs A Plot
URL: ../../../library/sma/html/plot.confband.text.html

Entry: plot.cor
Aliases: plot.cor
Keywords: Microarray, correlation matrix, image. hplot
Description: Red and Green Color Image of Correlation Matrix
URL: ../../../library/sma/html/plot.cor.html

Entry: plot.mat
Aliases: plot.mat
Keywords: hplot Microarray, image of data matrix.
Description: Red and Green Color Image of Data Matrix
URL: ../../../library/sma/html/plot.mat.html

Entry: plot.mva
Aliases: plot.mva
Keywords: microarray hplot
Description: M vs. A Plot
URL: ../../../library/sma/html/plot.mva.html

Entry: plot.qq
Aliases: plot.qq
Keywords: hplot microarray, histogram, qqplot.
Description: Histogram and Normal Quantile-Quantile plot
URL: ../../../library/sma/html/plot.qq.html

Entry: plot.qqline
Aliases: plot.qqline
Keywords: Q-Q plots, quartiles
Description: Add Line Going Through the Quantiles of a Q-Q Plot
URL: ../../../library/sma/html/plot.qqline.html

Entry: plot.scale.box
Aliases: plot.scale.box
Keywords: hplot boxplots, microarray
Description: Box plots for microarray
URL: ../../../library/sma/html/plot.scale.box.html

Entry: plot.smooth.line
Aliases: plot.smooth.line
Keywords: aplot microarray, lowess.
Description: Adding Lowess Lines to Current Plot
URL: ../../../library/sma/html/plot.smooth.line.html

Entry: plot.spatial
Aliases: plot.spatial draw.image.func spatial.func
Keywords: microarray, spatial.
Description: Spatial Representation of Microarray Spot Statistics
URL: ../../../library/sma/html/plot.spatial.html

Entry: plot.svb
Aliases: plot.svb svb.func
Keywords: hplot microarray, background
Description: Plot of Signal vs. Background
URL: ../../../library/sma/html/plot.svb.html

Entry: plot.t2
Aliases: plot.t2
Keywords: microarray, ttest. hplot
Description: Diagnostic Plots for Two-Sample t-statistics
URL: ../../../library/sma/html/plot.t2.html

Entry: read.genepix
Aliases: read.genepix
Keywords: microarray, GenePix. file
Description: Reading in Data Generated by the Image Analysis Package GenePix.
URL: ../../../library/sma/html/read.genepix.html

Entry: read.spot
Aliases: read.spot
Keywords: file microarray, Spot, GenePix.
Description: Reading in Data Generated by the Image Analysis Package Spot
URL: ../../../library/sma/html/read.spot.html

Entry: rgcolors.func
Aliases: rgcolors.func
Keywords: color Microarray, RGB image.
Description: Red and Green Color Specification
URL: ../../../library/sma/html/rgcolors.func.html

Entry: internal functions
Aliases: mouse.lratio mouse.data mouse.setup cl mouse.t2 c.min chen.poly chur.norm.func dc.min in.func lods.func nploglikderiv sq.func stat.ChurSap.ma va.func chen.func.rotate chen.plot.rotate chur.M.to.e.func chur.em.func chur.pdf chur.wrapper.func func.em givelim lf.func lod2 newton.plot.rotate nploglik setup.bayesian sq2.func stat.Chen.ma stat.Newton.ma va2.func
Keywords: methods
Description: Internal sma functions
URL: ../../../library/sma/html/sma-internal.html

Entry: stat.bayesian
Aliases: stat.bayesian
Keywords: models microarray, bayesian, lodsratio
Description: Calculates an Odds Ratio of Each Gene in a Multi-slide microarray Experiment
URL: ../../../library/sma/html/stat.bayesian.html

Entry: stat.bwss
Aliases: stat.bwss
Keywords: models Microarray, BSS, WSS, sum of squares.
Description: Between and Within Group Sum of Squares Calculation
URL: ../../../library/sma/html/stat.bwss.html

Entry: stat.Chen
Aliases: stat.Chen
Keywords: models microarray, Chen
Description: Apply Chen's single slide method
URL: ../../../library/sma/html/stat.Chen.html

Entry: stat.ChurSap
Aliases: stat.ChurSap
Keywords: microarray, Churchill, Sapir models
Description: Apply Sapir and Churchills single slide method
URL: ../../../library/sma/html/stat.ChurSap.html

Entry: stat.diag.da
Aliases: stat.diag.da
Keywords: models Microarray, discriminant analysis, maximum likelihood, classification.
Description: Diagonal Discriminant Analysis
URL: ../../../library/sma/html/stat.diag.da.html

Entry: stat.gnames
Aliases: stat.gnames
Keywords: misc microarray.
Description: Sort Genes According to the Value of a Statistic
URL: ../../../library/sma/html/stat.gnames.html

Entry: stat.ma
Aliases: stat.ma ma.func norm.l.func norm.pin.func norm.scale.func
Keywords: manip microarray, log ratio.
Description: Calculation of log Intensity Ratios and Average log Intensities
URL: ../../../library/sma/html/stat.ma.html

Entry: stat.Newton
Aliases: stat.Newton
Keywords: models
Description: Apply Newtons single slide method
URL: ../../../library/sma/html/stat.Newton.html

Entry: stat.norm.exp
Aliases: stat.norm.exp
Keywords: manip microarray, log ratio, normalization.
Description: Normalization of log Intensity Ratios across slides / experiments.
URL: ../../../library/sma/html/stat.norm.exp.html

Entry: stat.t2
Aliases: stat.t2 t2stat.func
Keywords: htest T-test.
Description: Two-sample t-statistics
URL: ../../../library/sma/html/stat.t2.html

Entry: write.spot
Aliases: write.spot
Keywords: file microarray, Spot, Genepix.
Description: Writing in Data Generated by the Image Analysis Package Spot
URL: ../../../library/sma/html/write.spot.html

