AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

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Processing and Analysis of Agilent microRNA data

Author
Pedro Lopez-Romero <plopez@cnic.es>
Date of publication
None
Maintainer
Pedro Lopez-Romero <plopez@cnic.es>
License
GPL-3
Version
2.24.0

View on Bioconductor

Man 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)
dimnames.uRNAList
Retrieve the Dimension Names of an uRNAList Object
dim.uRNAList
Retrieve the Dimensions 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
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
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
uRNAList - class
writeEset
Writes the expression data matrix of an ExpressionSet object...

Files in this package

AgiMicroRna/DESCRIPTION
AgiMicroRna/NAMESPACE
AgiMicroRna/R
AgiMicroRna/R/AgiMicroRNA-classes.R
AgiMicroRna/R/DEG.print.info.R
AgiMicroRna/R/HeatMapMicroRna.R
AgiMicroRna/R/MA.plot.miRNA.R
AgiMicroRna/R/PCAplotMicroRna.R
AgiMicroRna/R/RleMicroRna.R
AgiMicroRna/R/basicLimma.R
AgiMicroRna/R/boxplotMicroRna.R
AgiMicroRna/R/cv.array.R
AgiMicroRna/R/cvArray.R
AgiMicroRna/R/esetMicroRna.R
AgiMicroRna/R/filter.IsGeneDetected.R
AgiMicroRna/R/filter.control.miRNA.R
AgiMicroRna/R/filter.wellaboveNEG.miRNA.R
AgiMicroRna/R/filterFLAG.micro.R
AgiMicroRna/R/filterMicroRna.R
AgiMicroRna/R/filterWellAboveSIGNALv2.R
AgiMicroRna/R/getDecideTests.R
AgiMicroRna/R/getTDRows2.R
AgiMicroRna/R/hierclusMicroRna.R
AgiMicroRna/R/miRNA.htmlpage.R
AgiMicroRna/R/mvaBASIC.R
AgiMicroRna/R/mvaMicroRna.R
AgiMicroRna/R/paste.character.R
AgiMicroRna/R/plotDensityMicroRna.R
AgiMicroRna/R/pvalHistogram.R
AgiMicroRna/R/qcPlots.R
AgiMicroRna/R/read.agiMicroRna.R
AgiMicroRna/R/readMicroRnaAFE.R
AgiMicroRna/R/readTargets.R
AgiMicroRna/R/rmaMicroRna.R
AgiMicroRna/R/significantMicroRna.R
AgiMicroRna/R/subsetting.R
AgiMicroRna/R/tgsMicroRna.R
AgiMicroRna/R/tgsNormalization.R
AgiMicroRna/R/write.LIST.miRNA.R
AgiMicroRna/R/write.control.out.miRNA.R
AgiMicroRna/R/write.filt.out.miRNA.R
AgiMicroRna/R/writeEset.R
AgiMicroRna/build
AgiMicroRna/build/vignette.rds
AgiMicroRna/data
AgiMicroRna/data/datalist
AgiMicroRna/data/dd.micro.rda
AgiMicroRna/data/ddPROC.rda
AgiMicroRna/data/targets.micro.rda
AgiMicroRna/inst
AgiMicroRna/inst/doc
AgiMicroRna/inst/doc/AgiMicroRna.R
AgiMicroRna/inst/doc/AgiMicroRna.Rnw
AgiMicroRna/inst/doc/AgiMicroRna.pdf
AgiMicroRna/man
AgiMicroRna/man/HeatMapMicroRna.Rd
AgiMicroRna/man/PCAplotMicroRna.Rd
AgiMicroRna/man/RleMicroRna.Rd
AgiMicroRna/man/basicLimma.Rd
AgiMicroRna/man/boxplotMicroRna.Rd
AgiMicroRna/man/cvArray.Rd
AgiMicroRna/man/dd.micro.Rd
AgiMicroRna/man/ddPROC.Rd
AgiMicroRna/man/dim.uRNAList.Rd
AgiMicroRna/man/dimnames.uRNAList.Rd
AgiMicroRna/man/esetMicroRna.Rd
AgiMicroRna/man/filterMicroRna.Rd
AgiMicroRna/man/getDecideTests.Rd
AgiMicroRna/man/hierclusMicroRna.Rd
AgiMicroRna/man/mvaBASIC.Rd
AgiMicroRna/man/mvaMicroRna.Rd
AgiMicroRna/man/plotDensityMicroRna.Rd
AgiMicroRna/man/pvalHistogram.Rd
AgiMicroRna/man/qcPlots.Rd
AgiMicroRna/man/readMicroRnaAFE.Rd
AgiMicroRna/man/readTargets.Rd
AgiMicroRna/man/rmaMicroRna.Rd
AgiMicroRna/man/significantMicroRna.Rd
AgiMicroRna/man/summary.uRNAList.Rd
AgiMicroRna/man/targets.micro.Rd
AgiMicroRna/man/tgsMicroRna.Rd
AgiMicroRna/man/tgsNormalization.Rd
AgiMicroRna/man/uRNAList.Rd
AgiMicroRna/man/writeEset.Rd
AgiMicroRna/vignettes
AgiMicroRna/vignettes/AgiMicroRna.Rnw
AgiMicroRna/vignettes/AgiMicroRna.bib