arrayQualityMetrics: Quality metrics report for microarray data sets
Version 3.32.0

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

Browse man pages Browse package API and functions Browse package files

AuthorAudrey Kauffmann, Wolfgang Huber
Bioconductor views Microarray OneChannel QualityControl ReportWriting TwoChannel
Date of publicationNone
MaintainerAudrey Kauffmann <akauffmann.bioinfo@gmail.com>
LicenseLGPL (>= 2)
Version3.32.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("arrayQualityMetrics")

Man pages

aqmReportModule: Class to contain all the information to render a quality...
aqm.writereport: Write a quality report
arrayQualityMetrics: Quality metrics for microarray experiments
modulefunctions: Functions for computing quality report modules.
outlierDetection: Represents the results from applying an outlier detection...
outliers: Helper functions for outlier detection and reporting in...
prepdata: Compute useful summary statistics from a data object.
XYfromGAL: Computing the coordinates of the spots on a slide

Functions

addXYfromGAL Man page Source code
addXYfromGAL-methods Man page
annotateSvgGrid Source code
annotateSvgPlot Source code
annotationTable Source code
applyDyeSwap Source code
aqm.boxplot Man page Source code
aqm.density Man page Source code
aqm.heatmap Man page Source code
aqm.maplot Man page Source code
aqm.meansd Man page Source code
aqm.nuse Man page Source code
aqm.outliers Source code
aqm.pca Man page Source code
aqm.pmmm Man page Source code
aqm.probesmap Man page Source code
aqm.qcstats Man page
aqm.rle Man page Source code
aqm.rnadeg Man page Source code
aqm.spatial Man page Source code
aqm.writereport Man page Source code
aqmReportModule Man page
aqmReportModule-class Man page
arrayQualityMetrics Man page Source code
boxplotOutliers Man page Source code
class:aqmReportModule Man page
class:outlierDetection Man page
cleanPhenoData Source code
dens Source code
dircreation Source code
figurePhrase Source code
intgroupColors Source code
introductoryNote Source code
logtransform Source code
makeEnding Source code
makeIndex Source code
makePlot Source code
makeSection Source code
makeTitle Source code
makeabscoord Source code
makecoordblock Source code
maximumLevels Source code
namedEmptyList Source code
oneColor Source code
outlierDetection Man page
outlierDetection-class Man page
outliers Man page Source code
prepaffy Man page Source code
prepdata Man page Source code
processMaxNumArrays Source code
renameNodes Source code
reportModule Source code
reportTable Source code
spatialplot Source code
toJSON_fromchar Source code
toJSON_frommatrix Source code
toJSON_fromvector Source code
toggleEnd Source code
toggleStart Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/XYfromGAL.r
R/affyspecific.r
R/annotateSvg.R
R/arrayQualityMetrics.r
R/boxplot.r
R/classes.R
R/density.r
R/globalParameters.R
R/heatmap.r
R/makeColors.R
R/maplot.r
R/meansd.r
R/outlier.R
R/pca.r
R/prepdata.r
R/probesmap.r
R/spatial.r
R/writereport.r
TODO
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/aqm.R
inst/doc/aqm.Rnw
inst/doc/aqm.pdf
inst/doc/arrayQualityMetrics.R
inst/doc/arrayQualityMetrics.Rnw
inst/doc/arrayQualityMetrics.pdf
inst/javascript
inst/javascript/arrayQualityMetrics.css
inst/javascript/arrayQualityMetrics.js
inst/scripts
inst/scripts/run.sh
inst/scripts/testRGListAndMAList.R
inst/scripts/testbeadarray.R
inst/scripts/testcd8.R
man
man/XYfromGAL.Rd
man/aqm.writereport.Rd
man/aqmReportModule.Rd
man/arrayQualityMetrics.Rd
man/modulefunctions.Rd
man/outlierDetection.Rd
man/outliers.Rd
man/prepdata.Rd
vignettes
vignettes/aqm.Rnw
vignettes/arrayQualityMetrics.Rnw
vignettes/arrayQualityMetrics.bib
vignettes/arraymetadatatable.png
vignettes/pcaplot.png
arrayQualityMetrics documentation built on May 20, 2017, 10:13 p.m.