affy (version 1.50.0)

affyQAReport: Generate a QA Report for Affymetrix arrays

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.

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.

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.

Examples

library("affydata")
   data("Dilution")
   affyQAReport(Dilution)