calculateDetection {beadarray} | R Documentation

## Calculate detection scores

### Description

Function to calculate detection scores for summarized data if they are not available.

### Usage

    calculateDetection(BSData)

### Arguments

`BSData` | An ExpressionSetIllumina object

### Details

The function implements Illumina's method for calculating the detection scores for all bead types on a given array. Within an array, Illumina discard negative control bead-types whose summary values are more than three MADs from the median for the negative controls. Illumina then rank the summarized intensity for each other bead-type against the summarized values for the remaining negative control bead-types and calculate a detection p-value 1-R/N, where R is the relative rank of the bead intensity when compared to the $N$ remaining negative controls. Thus, if a particular bead has higher intensity than all the negative controls it will be assigned a value of 0. This calculation is repeated for all arrays stored in the BSData object.

### Value

A modified version of BSData is returned with the detection slot filled with the newly created scores.

### Author(s)

Mark Dunning and Andy Lynch

[Package beadarray version 1.10.0 Index]