limma (version 3.28.14)

plotSA: Sigma vs A plot for microarray linear model

Description

Plot log residual standard deviation versus average log expression for a fitted microarray linear model.

Usage

plotSA(fit, xlab="Average log-expression", ylab="log2(sigma)", zero.weights=FALSE, pch=16, cex=0.2, ...)

Arguments

fit

an MArrayLM object.

xlab

character string giving label for x-axis

ylab

character string giving label for y-axis

pch

vector or list of plotting characters. Default is integer code 16 which gives a solid circle.

cex

numeric expansion factor for plotting character. Defaults to 0.2.

zero.weights

logical, should spots with zero or negative weights be plotted?

...

any other arguments are passed to plot

Value

Details

This plot is used to check the mean-variance relationship of the expression data, after fitting a linear model.

See points for possible values for pch and cex.

See Also

An overview of diagnostic functions available in LIMMA is given in 09.Diagnostics.