summarize.probe {Agi4x44PreProcess} | R Documentation

## Replicated Probes Summarization

### Description

Computes Median of Replicated non-control probes

### Usage

    summarize.probe(ddFILT, makePLOT, targets)

### Arguments

`ddFILT` | RGlist, usually containing Normalized and Filtered data
`makePLOT` | LOGICAL: If True it makes graphs
`targets` | data.frame with the target structure

### Details

Normally, the Agilent 4 x 44 chips contain a set of non-control probes that are replicated up to ten times. These probes are spread over the chip and allow measuring the chip reproducibility in terms of the coefficient of variation ( of the array. A lower CV median indicates a better reproducibility of the array. It uses an RGList as an input and it produces another RGList where each set of replicated non-control probes have been collapsed into a single value computed as the median of the probes intensities belonging to the same set. Normally, the input RGList is the 'filtered data', but other RGList can be used as inputs. This is an optional step.

### Value

RGList

### Author(s)

Pedro Lopez-Romero

### See Also

`CV.rep.probes`

### Examples

    ## Not run:
            data(targets)
            data(dd)
            ddPROC=summarize.probe(dd,makePLOT=TRUE,targets)
    ## End(Not run)

[Package Agi4x44PreProcess version 1.2.0 Index]