CV.rep.probes {Agi4x44PreProcess}R Documentation

Non-control replicated Probes identication

Description

Computes the non-control replicated probes

Usage

CV.rep.probes(ddDUP, annotation.package, foreground, raw.data, writeR,targets)

Arguments

ddDUP An RGList
annotation.package a character specifying the AGI annotation package: 'hgug4112a.db','mgug4122a.db'
foreground a character specifying the signal from wich the CV is calculated: 'MeanSignal' or 'ProcessedSignal'
raw.data logical, TRUE if the RGList contains the RAW data
writeR logical, TRUE to write the REPORT FILE 'Probe.Sets.txt'
targets data.frame containing the TARGET file

Details

Agilent arrays contain a number of non-control probes replicated up to ten times spread accross the array. This allows computing the of coefficient of variation) for each array. The CV is computed for every set of replicated probes. CV median is reported as the array CV. A lower CV median indicates a better array reproducibility.

Value

A txt file 'Probe.Sets.txt' that contains PROBE, number of replicates, ACCNUM code, SYMBOL code, DESCRIPTION of the gene, and probe of the arrays A boxplot that shows CV distribution computed for every set of replicated probes

Author(s)

Pedro Lopez-Romero

Examples

## Not run: 
        data(dd)
        data(targets)
        library(hgug4112a.db)
        CV.rep.probes(dd,"hgug4112a.db",
                foreground="MeanSignal",raw.data=TRUE,writeR=TRUE,targets)
## End(Not run)

[Package Agi4x44PreProcess version 1.2.0 Index]