calculateDetection {beadarray} | R Documentation |
Function to calculate detection scores for summarized data if they are not available.
calculateDetection(BSData)
BSData |
An ExpressionSetIllumina object |
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.
A modified version of BSData is returned with the detection slot filled with the newly created scores.
Mark Dunning and Andy Lynch