Processing and Differential Expression Analysis of Agilent microRNA chips


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Documentation for package ‘AgiMicroRna’ version 2.48.0

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basicLimma Linear models Using limma
boxplotMicroRna Boxplot
cvArray Coefficient of variation of replicated probes within array
dd.micro data example (uRNAList)
ddPROC Processed miRNA data (uRNAList)
dim.uRNAList Retrieve the Dimensions of an uRNAList Object
dimnames.uRNAList Retrieve the Dimension Names of an uRNAList Object
dimnames<-.uRNAList Retrieve the Dimension Names of an uRNAList Object
esetMicroRna ExpressionSet object from a uRNAList
filterMicroRna Filtering Genes
getDecideTests Differential expression analysis an multiplicity of the tests
HeatMapMicroRna HeatMap
hierclusMicroRna Hierarchical clustering
length.uRNAList Retrieve the Dimensions of an uRNAList Object
mvaBASIC MVA plot
mvaMicroRna MA plot
PCAplotMicroRna PCA plot
plotDensityMicroRna Density Plots of Intensity Signals
pvalHistogram Histogram of the p values
qcPlots Plots for Quality Assessment
readMicroRnaAFE Read Agilent Feature Extraction txt data files
readTargets read the target file
RleMicroRna Relative Log Expression
rmaMicroRna Getting the Total Gene Signal by RMA algorithm
show-method uRNAList - class
significantMicroRna Summarize Differential Expression Results
summary.uRNAList Summaries of Microarray Data Objects
targets.micro Example of target file
tgsMicroRna Getting the Total Gene Signal
tgsNormalization Normalization Between Arrays
uRNAList-class uRNAList - class
writeEset Writes the expression data matrix of an ExpressionSet object in a txt file