# Processing and Differential Expression Analysis of Agilent microRNA chips

## Documentation for package ‘AgiMicroRna’ version 2.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## 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