arrayQualityMetrics: Quality metrics report for microarray data sets

Share:

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.

Author
Audrey Kauffmann, Wolfgang Huber
Date of publication
None
Maintainer
Audrey Kauffmann <akauffmann.bioinfo@gmail.com>
License
LGPL (>= 2)
Version
3.30.0

View on Bioconductor

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

Files in this package

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