LMGene (version 2.28.0)

plotMeanSD: Plotting function for gene means and standard deviations

Description

Plots the row standard deviation of a matrix of expression data against the row mean, or the rank of the row mean.

Usage

plotMeanSD(indata, by.rank = TRUE, line = FALSE, ymax = NULL)

Arguments

indata

An object of class matrix, data.frame, ExpressionSet, or AffyBatch

by.rank

If TRUE, the row standard deviations are plotted against the ranks of the row means. Otherwise, the row standard deviations are plotted against the row means themselves.

line

If TRUE, a lowess smoother line is drawn on the plot.

ymax

The upper limit for the plot y-axis. If missing, axis limits are generated automatically by plot.

Value

NULL

Details

Generates a scatter plot of the row standard deviations of a matrix of expression data against the row means or ranks of the row means.

Examples

library(LMGene)
library(Biobase)

data(sample.eS)
# transform data
trans.eS <- transeS(sample.eS, lambda = 727, alpha = 56)

# plot SD against rank of mean
plotMeanSD(trans.eS, line = TRUE)
plotMeanSD(sample.eS, line = TRUE, ymax = 1000)