summary.spotseg {spotSegmentation} | R Documentation |
Summary method for the spotseg
function.
Gives the estimates of foreground and background intensity
obtained from microarray spot segmentation via model-based clustering.
## S3 method for class 'spotseg': summary(object,...)
object |
An object of class "spotseg" , which is the
output of the function spotseg . |
... |
Unused, but required by generic "summary" method. |
A list with two components, "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.
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.
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)