affyQAReport: Generate a QA Report for Affymetrix arrays

In affyQCReport: QC Report Generation for affyBatch objects

Description

These functions provide a method for creating, viewing and removing QA reports on an experiment run on Affymetrix CEL files.

Usage

affyQAReport(affyB, output = "pdf", outdir = file.path(getwd(), "affyQA"), 
       overwrite = FALSE, repName)
rmQAReport(x)
openQAReport(x)

Arguments

affyB	An instance of the AffyBatch class.
output	Type of output wanted, currently only pdf is supported.
outdir	The directory (or folder) where output will be directed.
overwrite	Whether an existing report, with the same name, should be overwritten.
repName	A character string indicating the name of the report.
x	A character string containing the location of the directory holding the report.

Details

A wide variety of tools from different packages are used, in conjunction with Sweave tools to produce an integrated document with various statistics that should help determine whether there are data quality problems with the data.

This package only works for Affymetrix data. It requires a working LaTeX implementation and so is not likely to work on Windows platforms, and in some cases on OS X unless the user has installed these tools.

Sample names that have an underscore in them have it replaced by a dot. Underscore causes a number of problems with Latex, if it is not escaped.

Value

A list with the following components is returned.

qcStats	The QC statistics computed by the simpleaffy package.
affyPLM	The QC statistics computed by the affyPLM package.
MADS	The computed MAD statistic on the ‘M’ values from an M-A decomposition.
loc	The location (directory/folder) containing the report.
name	The name of the report.

Author(s)

R. Gentleman

Examples

## Not run: 
   library("affydata")
   data("Dilution")
   affyQAReport(Dilution)

## End(Not run)

affyQCReport documentation built on Nov. 8, 2020, 5:40 p.m.