Package: AgiMicroRna 2.63.0

Pedro Lopez-Romero

AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Processing and Analysis of Agilent microRNA data

Authors:Pedro Lopez-Romero <[email protected]>

# Install 'AgiMicroRna' in R:

install.packages('AgiMicroRna', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On BioConductor:AgiMicroRna-2.63.0(bioc 3.24)AgiMicroRna-2.62.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:bd9b1c3968. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	274
linux-devel-x86_64	WARNING	527
source / vignettes	OK	384
linux-release-x86_64	WARNING	424
macos-release-arm64	WARNING	279
macos-oldrel-arm64	WARNING	242
windows-devel	WARNING	426
windows-release	WARNING	394
windows-oldrel	WARNING	430
wasm-release	OK	241

Last update: 2013-11-01
Started: 2013-11-01

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