plotMeanSD: Plotting function for gene means and standard deviations

In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

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.

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.

Value

NULL

Author(s)

Rachel Chen and Blythe Durbin-Johnson

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)

LMGene documentation built on April 28, 2020, 8:01 p.m.