summary.spotseg: Microarray Spot Segmentation Summary

Description

Summary method for the spotseg function. Gives the estimates of foreground and background intensity obtained from microarray spot segmentation via model-based clustering.

Usage

"summary"(object,...)

Arguments

object

An object of class "spotseg", which is the output of the function spotseg.

...

Unused, but required by generic "summary" method.

Value

"channel1" and "channel2" each of which has subcomponents "background" and "foreground", each of which in turn has subcomponents "mean" and "median", giving the mean and median estimates of background and foreground for each channel. There will be missing entries (value NA) whenever no foreground is detected.

References

Q. Li, C. Fraley, R. Bumgarner, K. Y. Yeung, and A. Raftery\ Robust model-based segmentation of microarray images,\ Technical Report No.~473, Department of Statistics, University of Washington, January 2005.

Examples

Run this code

data(spotSegTest)

# columns of spotSegTest:
#  1 intensities from the Cy3 (green) channel
#  2 intensities from the Cy5 (red) channel

dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05 

chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)

hivGrid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)

library(mclust)

hivSeg <- spotseg( chan1, chan2, hivGrid$rowcut, hivGrid$colcut)

hivSummary <- summary(hivSeg)