imageProcessing: Image processing functions
In beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description Usage Arguments Value Author(s) References

Functions for obtaining bead intensity values from raw tiff images. The three commands with the illumina prefix attempt to emulate the image processing implemented by Illumina. The medianBackground function implements a more robust background calculation recommended by Smith et al.

illuminaForeground(pixelMatrix, beadCoords)
illuminaBackground(pixelMatrix, beadCoords)
illuminaSharpen(pixelMatrix)

medianBackground(pixelMatrix, beadCoords)

`pixelMatrix`	A matrix storing the individual pixel values of an image. Intended to be created by `readTIFF`, although any matrix can be passed as input.
`beadCoords`	Two column matrix with each row containing a pair of coordinates representing a bead centre.

illuminaForeground, illuminaBackground and medianBackground return a vector of intensity values, with one entry for every row in the beadCoords argument. Any pairs of coordinates that fall outside the dimensions of the image return NA.

illuminaSharpen returns a matrix with the same dimensions as the pixelMatrix argument.

Mike Smith

Smith ML, Dunning MJ, Tavare S, Lynch AG. Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics (2010) 11:208

beadarray documentation built on Nov. 8, 2020, 4:51 p.m.