Exploratory analysis for two-color spotted microarray data

boxplot | Boxplots for cDNA microarray spot statistics |

bracketMethods | Subsetting methods for microarray objects |

cbind | Combine marrayRaw, marrayNorm or marrayInfo Objects |

checkTargetInfo | Verifying the order between intensities matrix and target... |

coerce-methods | Coerce an object to belong to a given microarray class |

dim | Retrieve the Dimensions of an marrayRaw, marrayNorm or... |

findID | Find ID when given an accession number |

htmlPage | Display gene list as a HTML page |

image | Color image for cDNA microarray spot statistics |

ma2D | Stratified bivariate robust local regression |

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 |

maCompPlate | Generate plate IDs |

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... |

maDotsMatch | Replace default arguments of a function by user supplied... |

maGenControls | Generating a vector recording the control status of the... |

maGeneTable | Table of spot coordinates and gene names |

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 |

maLegendLines | Add a legend to a plot |

maLoess | Stratified univariate robust local regression |

maLoessLines | Add smoothed fits to a plot |

maMAD | Stratified MAD calculation |

maMed | Stratified median calculation |

maNA | Basic Statistical Functions for Handling Missing Values |

maNorm | Simple location and scale normalization function |

maNorm2D | 2D spatial location normalization function |

maNormLoess | Intensity dependent location normalization function |

maNormMAD | MAD scale normalization function |

maNormMain | Main function for location and scale normalization of cDNA... |

maNormMed | Median location normalization function |

maNormScale | Simple scale normalization function |

maNum2Logic | Convert a numeric vector of indices to a logical vector |

maPalette | Microarray color palette |

mapGeneInfo | Creating URL strings for external database links |

maPlot | Scatter-plots for cDNA microarray spot statistics |

maPlot.func | Scatter-plots with fitted curves and text |

marrayInfo-class | Class "marrayInfo", description of target samples or spotted... |

marray-internal | Internal marray functions |

marrayLayout-class | Class "marrayLayout", classes and methods for layout... |

marrayNorm-class | Class "marrayNorm", classes and methods for... |

marrayRaw-class | Class "marrayRaw", classes and methods for pre-normalization... |

maSelectGnames | Select genes according to the values of a few different... |

maText | Highlight points on a plot |

maTop | Identify extreme values |

maTwoSamples | Changing signs for two sample analysis |

opVersionID | Determine the operon oligo set ID |

plotMA | Scatter-plots for cDNA microarray spot statistics |

print-methods | Printing summary methods for microarray objects |

read.Galfile | Reading GenePix Gal file |

read.marrayInfo | Create objects of class marrayInfo |

read.marrayLayout | Create objects of class marrayLayout |

read.marrayRaw | Create objects of class "marrayRaw" |

rm.na | Remove missing values |

showLargeObject | Show Large Data Object - class |

stat.confband.text | Rank genes according to the value of a statistic. |

stat.gnames | Sort Genes According to the Value of a Statistic |

swirl | Gene expression data from Swirl zebrafish cDNA microarray... |

write.list | Data Output |

write.marray | Data Output |

write.xls | Data Output |

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