plotMvsM.MAData: Plots the log-ratios for one slide versus another

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Plots the log-ratios for one slide versus another.

Usage

## S3 method for class 'MAData'
plotMvsM(this, slides=NULL, include=NULL, exclude=NULL, pch="auto", xlim=NULL, ylim=xlim, xlab=NULL, ylab=NULL, ..., style=NULL)

Arguments

slides	vector of two slide indices to be plotted against each other.
pch	The plot symbol.
xlim, ylim	The visible range on the x and the y axis.
xlab, ylab	The labels of the x and the y axis.
...	Other arguments accepted by plot.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

*pointsMvsM(). For more information see MAData.

Examples

# Load some example data
SMA$loadData("mouse.data")
layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
raw <- RawData(mouse.data, layout=layout)

# Get the signal
ma <- getSignal(raw, bgSubtract=TRUE)

subplots(4)

plotMvsM(ma, slides=c(1,2), xlim=c(-1,1)*3, pch=".")
points(ma, slides=c(3,4), col="red", pch=".")
points(ma, slides=c(5,6), col="blue", pch=".")
abline(a=0, b=1, lty=2)
title(main="Three different (M,M) pairs")


normalizeWithinSlide(ma, method="l")
normalizeAcrossSlides(ma)

plotMvsM(ma, slides=c(1,2), xlim=c(-1,1)*3, pch=".")
points(ma, slides=c(3,4), col="red", pch=".")
points(ma, slides=c(5,6), col="blue", pch=".")
abline(a=0, b=1, lty=2)
title(main="Same after lowess normalization")

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.