ma2D |
Stratified bivariate robust local regression |
maA |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maA-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maA-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maA<- |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maA<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maBoxplot |
Boxplots for cDNA microarray spot statistics |
maColorBar |
Calibration bar for color images |
maCompCoord |
Generate grid and spot matrix coordinates |
maCompInd |
Generate spot indices |
maCompLayout |
Generate a marrayLayout object |
maCompNormA |
Weights for composite normalization |
maCompNormEq |
Weights for composite normalization |
maCompPlate |
Generate plate IDs |
maControls |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maControls-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maControls-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maControls-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maControls<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maControls<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maControls<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maControls<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maCoord2Ind |
Convert grid and spot matrix coordinates to spot indices |
maDefaultPar |
Default graphical parameters for microarray objects |
maDotsDefaults |
Replace graphical default parameters by user supplied parameters |
maDotsMatch |
Replace default arguments of a function by user supplied values |
maGb |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGb-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGb<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGb<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGenControls |
Generating a vector recording the control status of the spotted probe |
maGeneTable |
Table of spot coordinates and gene names |
maGf |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGf-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGf<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGf<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGnames |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGnames-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maGnames-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGnames<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGnames<--method |
Class "marrayInfo", description of target samples or spotted probe |
maGridCol |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maGridCol-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maGridCol-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maGridCol-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maGridRow |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maGridRow-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maGridRow-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maGridRow-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maImage |
Color image for cDNA microarray spot statistics |
maImage.func |
Color image for cDNA microarray spot statistics |
maInd2Coord |
Convert spot indices to grid and spot matrix coordinates |
maInfo |
Class "marrayInfo", description of target samples or spotted probe |
maInfo-method |
Class "marrayInfo", description of target samples or spotted probe |
maInfo<- |
Class "marrayInfo", description of target samples or spotted probe |
maInfo<--method |
Class "marrayInfo", description of target samples or spotted probe |
maLabels |
Class "marrayInfo", description of target samples or spotted probe |
maLabels-method |
Class "marrayInfo", description of target samples or spotted probe |
maLabels<- |
Class "marrayInfo", description of target samples or spotted probe |
maLabels<--method |
Class "marrayInfo", description of target samples or spotted probe |
maLayout |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLayout-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maLayout-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLayout<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLayout<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maLegendLines |
Add a legend to a plot |
maLG |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLG-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maLG-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLoess |
Stratified univariate robust local regression |
maLoessLines |
Add smoothed fits to a plot |
maLowessLines |
Add smoothed fits to a plot |
maLR |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maLR-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maLR-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maM |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maM-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maM-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maM<- |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maM<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMAD |
Stratified MAD calculation |
maMed |
Stratified median calculation |
maMloc |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMloc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMloc<- |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMloc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMscale |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMscale-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMscale<- |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maMscale<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNgc |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgc-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNgc-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNgc<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgc<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNgc<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNgr |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgr-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgr-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNgr-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNgr<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgr<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNgr<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNgr<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNorm |
Simple location and scale normalization function |
maNorm2D |
2D spatial location normalization function |
maNormCall |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNormCall-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNormLoess |
Intensity dependent location normalization function |
maNormMAD |
MAD scale normalization function |
maNormMain |
Main function for location and scale normalization of cDNA microarray |
maNormMed |
Median location normalization function |
maNormScale |
Simple scale normalization function |
maNotes |
Class "marrayInfo", description of target samples or spotted probe |
maNotes-method |
Class "marrayInfo", description of target samples or spotted probe |
maNotes-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNotes-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNotes-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNotes<- |
Class "marrayInfo", description of target samples or spotted probe |
maNotes<--method |
Class "marrayInfo", description of target samples or spotted probe |
maNotes<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNotes<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNotes<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsamples |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsamples-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNsamples-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsc |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsc-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNsc-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsc<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsc<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNsc<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNspots |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNspots-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNspots-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNspots-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNspots<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNspots<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNspots<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNspots<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsr |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsr-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsr-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNsr-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNsr<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsr<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maNsr<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maNsr<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maNum2Logic |
Convert a numeric vector of indices to a logical vector |
maPalette |
Microarray color palette |
mapGeneInfo |
Creating URL strings for external database links |
maPlate |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPlate-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPlate-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maPlate-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maPlate<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPlate<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPlate<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maPlate<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maPlot |
Scatter-plots for cDNA microarray spot statistics |
maPlot.func |
Scatter-plots with fitted curves and text |
maPrintTip |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPrintTip-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maPrintTip-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maPrintTip-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRb |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRb-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRb<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRb<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRf |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRf-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRf<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maRf<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
marrayInfo |
Class "marrayInfo", description of target samples or spotted probe |
marrayInfo-class |
Class "marrayInfo", description of target samples or spotted probe |
marrayLayout |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
marrayLayout-class |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
marrayNorm |
Class "marrayNorm", classes and methods for post-normalization cDNA |
marrayNorm-class |
Class "marrayNorm", classes and methods for post-normalization cDNA |
marrayRaw |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
marrayRaw-class |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maSelectGnames |
Select genes according to the values of a few different statistics |
maSpotCol |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSpotCol-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSpotCol-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maSpotCol-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maSpotRow |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSpotRow-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSpotRow-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maSpotRow-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maSub |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSub-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSub-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maSub-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maSub<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSub<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA |
maSub<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maSub<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maTargets |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maTargets-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maTargets-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maTargets<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maTargets<--method |
Class "marrayInfo", description of target samples or spotted probe |
maText |
Highlight points on a plot |
maTop |
Identify extreme values |
maTwoSamples |
Changing signs for two sample analysis |
maW |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maW-method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maW-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maW<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
maW<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA |
maW<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA |
mean.na |
Basic Statistical Functions for Handling Missing Values |