imageLimma {genArise}R Documentation

Image Plot of Microarray

Description

Plot an image of colours representing the log intensity ratio for each spot on the array. This function can be used to explore whether there are any spatial effects in the data.

Usage

imageLimma(z, row, column, meta.row, meta.column,
low = NULL, high = NULL)

Arguments

z numeric vector or array. This vector can contain any spot statistics, such as log intensity ratios, spot sizes or shapes, or t-statistics. Missing values are allowed and will result in blank spots on the image
row rows in the microarray
column columns in the microarray
meta.row metarows in the microarray
meta.column metacolumns in the microarray
low color associated with low values of 'z'. May be specified as a character string such as '"green"', '"white"' etc, or as a rgb vector in which 'c(1,0,0)' is red, 'c(0,1,0)' is green and 'c(0,0,1)' is blue. The default value is '"green"' if 'zerocenter=T' or '"white"' if 'zerocenter=F'.
high color associated with high values of 'z'. The default value is '"red"' if 'zerocenter=T' or '"blue"' if 'zerocenter=F'.

Note

This function is based in the imageplot function from limma package.

References

Gordon K. Smyth (2004) "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments", Statistical Applications in Genetics and Molecular Biology: Vol. 3: No. 1, Article 3. http://www.bepress.com/sagmb/vol3/iss1/art3

Examples

data(Simon)
spot.data <- attr(Simon, "spotData")
M <- log(spot.data$Cy3, 2) - log(spot.data$Cy5, 2)
imageLimma(z = M, row = 23, column = 24, meta.row = 2, meta.column = 2,
low = NULL, high = NULL)

[Package genArise version 1.0.0 Index]