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	256
linux-devel-x86_64	WARNING	648
source / vignettes	OK	439
linux-release-x86_64	WARNING	575
macos-release-arm64	WARNING	353
macos-oldrel-arm64	WARNING	363
windows-devel	WARNING	421
windows-release	WARNING	403
windows-oldrel	WARNING	437
wasm-release	OK	203

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