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AgiMicroRna (version 2.22.0)

Processing and Differential Expression Analysis of Agilent microRNA chips

Description

Processing and Analysis of Agilent microRNA data

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Version

Version

2.22.0

License

GPL-3

Maintainer

Pedro LopezRomero

Last Published

February 15th, 2017

Functions in AgiMicroRna (2.22.0)

hierclusMicroRna

Hierarchical clustering
HeatMapMicroRna

HeatMap
tgsNormalization

Normalization Between Arrays
dd.micro

data example (uRNAList)
tgsMicroRna

Getting the Total Gene Signal
getDecideTests

Differential expression analysis an multiplicity of the tests
RleMicroRna

Relative Log Expression
basicLimma

Linear models Using limma
filterMicroRna

Filtering Genes
significantMicroRna

Summarize Differential Expression Results
boxplotMicroRna

Boxplot
cvArray

Coefficient of variation of replicated probes within array
targets.micro

Example of target file
qcPlots

Plots for Quality Assessment
readMicroRnaAFE

Read Agilent Feature Extraction txt data files
uRNAList-class

uRNAList - class
summary.uRNAList

Summaries of Microarray Data Objects
mvaBASIC

MVA plot
pvalHistogram

Histogram of the p values
mvaMicroRna

MA plot
rmaMicroRna

Getting the Total Gene Signal by RMA algorithm
readTargets

read the target file
plotDensityMicroRna

Density Plots of Intensity Signals
dim.uRNAList

Retrieve the Dimensions of an uRNAList Object
dimnames.uRNAList

Retrieve the Dimension Names of an uRNAList Object
writeEset

Writes the expression data matrix of an ExpressionSet object in a txt file
PCAplotMicroRna

PCA plot
esetMicroRna

ExpressionSet object from a uRNAList
ddPROC

Processed miRNA data (uRNAList)