Processing and Differential Expression Analysis of Agilent microRNA chips

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Documentation for package ‘AgiMicroRna’ version 2.59.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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