genArise (version 1.48.0)

imageLimma: 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'.

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