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arrayQuality (version 1.50.0)

Assessing array quality on spotted arrays

Description

Functions for performing print-run and array level quality assessment.

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Version

Version

1.50.0

License

LGPL

Maintainer

Agnes Paquet

Last Published

February 15th, 2017

Functions in arrayQuality (1.50.0)

gpQuality

Diagnostic plots and comparative boxplots for general hybridization
PRv9mers

Print Run Quality version 9mers
Internal functions

Internal arrayQuality functions
qualBoxplot

Comparative boxplot for general hybridization Quality Control
MmDEGenes

Known DE genes for Mouse quality hybridizations.
outlierDetection

Represents the results from applying an outlier detection criterion to the arrays.
qcScore

Quality Control score for general hybridization
slideQuality

Quality Control statistics for general hybridization
aqmReportModule

Class to contain all the information to render a quality report module.
readAgilent

Extraction of measures from Agilent (.txt) files.
maQualityPlots

Qualitative diagnostic plot for general hybridization
heeboQualityPlots

Qualitative diagnostic plot for general hybridization, specific to HEEBO set.
agQuality

Diagnostic plots and comparative boxplots for general hybridization, Agilent format
meeboQualityPlots

Qualitative diagnostic plot for general hybridization, specific to MEEBO set.
prdata

Example GPR files
readGPR

Reading GenePix gpr file
qualityScore

Quality Control score for general hybridization
arrayQualityMetrics

Quality metrics for microarray experiments
outliers

Helper functions for outlier detection and reporting in arrayQualityMetrics
spotQuality

Diagnostic plots and comparative boxplots for general hybridization, Spot format
gprDB

Reference slides for Mouse oligos hybridizations
meeboQuality

Diagnostics plots designed for MEEBO set controls
aqm.writereport

Write a quality report
globalQuality

Quality measures for general hybridization.
heeboQuality

Diagnostics plots designed for HEEBO set controls
scaleRefTable

General hybridization quality scaling
modulefunctions

Functions for computing quality report modules.
PRvQCHyb

Print run Quality version Quality Control Hybridization
readcontrolCode

Control status information
readSpikeTypes

Read Spike Types File
addXYfromGAL

Computing the coordinates of the spots on a slide
prepdata

Compute useful summary statistics from a data object.
readSpot

Extraction of measures from Spot (.spot) files.