| ma2D |
Stratified bivariate robust local regression |
| maA |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maA-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maA-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maA<- |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maA<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| 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 microarrays |
| maControls-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maControls-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maControls-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maControls<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maControls<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maControls<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maControls<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| 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 microarray intensity data |
| maGb-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGb<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGb<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGenControls |
Generating a vector recording the control status of the spotted probe sequences. |
| maGeneTable |
Table of spot coordinates and gene names |
| maGf |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGf-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGf<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGf<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGnames |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGnames-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGnames-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGnames<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGnames<--method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maGridCol |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridCol-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridCol-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGridCol-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGridRow |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridRow-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridRow-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGridRow-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| 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 sequences |
| maInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maInfo<- |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maInfo<--method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels<- |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels<--method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLayout |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maLayout-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLayout-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maLayout<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maLayout<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maLegendLines |
Add a legend to a plot |
| maLG |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maLG-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLG-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| 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 microarray intensity data |
| maLR-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLR-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maM |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maM-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maM-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maM<- |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maM<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMAD |
Stratified MAD calculation |
| maMed |
Stratified median calculation |
| maMloc |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMloc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMloc<- |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMloc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMscale |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMscale-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMscale<- |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMscale<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgc |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgc-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNgc<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgc<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNgr |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgr-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNgr<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgr<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNorm |
Simple location and scale normalization function |
| maNorm2D |
2D spatial location normalization function |
| maNormCall |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNormCall-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNormLoess |
Intensity dependent location normalization function |
| maNormMAD |
MAD scale normalization function |
| maNormMain |
Main function for location and scale normalization of cDNA microarray data |
| maNormMed |
Median location normalization function |
| maNormScale |
Simple scale normalization function |
| maNotes |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNotes-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNotes-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNotes<- |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes<--method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNotes<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNotes<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsamples |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsamples-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsamples-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsc |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsc-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsc<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsc<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNspots |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNspots-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNspots<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNspots<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsr |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsr-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsr<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsr<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| 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 microarrays |
| maPlate-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPlate-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPlate-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maPlate<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPlate<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPlate<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPlate<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| 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 microarrays |
| maPrintTip-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPrintTip-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPrintTip-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRf |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRf-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRf<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRf<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| marrayInfo |
Class "marrayInfo", description of target samples or spotted probe sequences |
| marrayInfo-class |
Class "marrayInfo", description of target samples or spotted probe sequences |
| marrayLayout |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| marrayLayout-class |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| marrayNorm |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| marrayNorm-class |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| marrayRaw |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| marrayRaw-class |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maSelectGnames |
Select genes according to the values of a few different statistics |
| maSpotCol |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotCol-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotCol-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSpotCol-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maSpotRow |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotRow-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotRow-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSpotRow-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maSub |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSub-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maSub<- |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub<--method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSub<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maTargets |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maTargets-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maTargets-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maTargets<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maTargets<--method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| 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 microarray intensity data |
| maW-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maW-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maW<- |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maW<--method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maW<--method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| mean.na |
Basic Statistical Functions for Handling Missing Values |