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]