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 1.4.0 Index]