weight.plot: Plot the weights of a given array using the spatial location...

In rama: Robust Analysis of MicroArrays

Description

Plot the weights of a given array using the spatial location of the genes on the slide.This function is a useful diagnostic tool.

Usage

weight.plot(mcmc.obj,coordinate,array=1)

Arguments

mcmc.obj	An object of class mcmc as returned by fit.model
coordinate	The coordinate of each gene on the corresponding array. The coordinates should be a two column integer valued matrix containing the row indices (column 1) and the column indices (column 2). The row indices should all be distinct. All indices should start at zero!
array	An integer corresponding to the array number to be plotted.

Value

The image plot of the weights. A small weight (bright color) correspond to an outlier.

Author(s)

Raphael Gottardo

References

Robust Estimation of cDNA Microarray Intensities with Replicates Raphael Gottardo, Adrian E. Raftery, Ka Yee Yeung, and Roger Bumgarner Department of Statistics, University of Washington, Box 354322, Seattle, WA 98195-4322

See Also

arrange.row

Examples

data(hiv)
### Initialize the proposals
mcmc.hiv<-fit.model(hiv[1:640,c(1:4)],hiv[1:640,c(5:8)],B=1000,min.iter=500,batch=1,shift=30,mcmc.obj=NULL,dye.swap=TRUE,nb.col1=2)
weight.plot(mcmc.hiv,hiv[1:640,9:10],array=3)

Example output

rama documentation built on Nov. 8, 2020, 8:02 p.m.