| ma2D |
Stratified bivariate robust local regression |
| maA |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maA,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maA,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maA<-,marrayNorm,matrix-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maControls,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maControls,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maControls<-,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maControls<-,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maControls<-,marrayRaw-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,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGb<-,marrayRaw,matrix-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGb<-,marrayRaw,NULL-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,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGf<-,marrayRaw,matrix-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGnames,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maGnames<-,marrayNorm,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maGnames<-,marrayRaw,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maGnames<-,marraySpots,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maGridCol |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridCol,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridCol,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGridCol,marrayRaw-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maGridRow,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maGridRow,marrayRaw-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,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maInfo<-,marrayInfo,data.frame-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels<-,marrayInfo,character-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maLabels<-,marrayInfo,numeric-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLayout,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maLayout<-,marrayNorm,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maLayout<-,marrayRaw,marrayLayout-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLG,marrayRaw-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maLR,marrayRaw-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maM,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maM<-,marrayNorm,matrix-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMloc<-,marrayNorm,matrix-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maMscale<-,marrayNorm,matrix-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgc,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNgc<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgc<-,marrayNorm,numeric-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgc<-,marrayRaw,numeric-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgr,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNgr<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNgr<-,marrayNorm,numeric-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNgr<-,marrayRaw,numeric-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,marrayNorm-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,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNotes,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNotes,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNotes<-,marrayInfo,character-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maNotes<-,marrayLayout,character-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNotes<-,marrayNorm,character-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNotes<-,marrayRaw,character-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsamples,marrayRaw-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsc,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsc<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsc<-,marrayNorm,numeric-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsc<-,marrayRaw,numeric-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNspots,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNspots<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNspots<-,marrayNorm,numeric-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNspots<-,marrayRaw,numeric-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsr,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maNsr<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maNsr<-,marrayNorm,numeric-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maNsr<-,marrayRaw,numeric-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPlate,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPlate,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maPlate<-,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPlate<-,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPlate<-,marrayRaw-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maPrintTip,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maPrintTip,marrayRaw-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,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb<-,marrayRaw,matrix-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRb<-,marrayRaw,NULL-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,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maRf<-,marrayRaw,matrix-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotCol,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSpotCol,marrayRaw-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSpotRow,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSpotRow,marrayRaw-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,marrayLayout-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSub,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maSub<-,marrayLayout,logical-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub<-,marrayLayout,numeric-method |
Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays |
| maSub<-,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maSub<-,marrayRaw-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maTargets,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maTargets<-,marrayNorm,marrayInfo-method |
Class "marrayInfo", description of target samples or spotted probe sequences |
| maTargets<-,marrayRaw,marrayInfo-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,marrayNorm-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maW,marrayRaw-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| maW<-,marrayNorm,matrix-method |
Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data |
| maW<-,marrayRaw,matrix-method |
Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data |
| mean.na |
Basic Statistical Functions for Handling Missing Values |