gplotMA: MA-plot: plot differences versus averages for Agilent...

In AlexeiSleptcov/aggi: Agilent arrays analisys (aggy)

Description

A generic function which produces an MA-plot for an object containing microarray data.

Usage

gplotMA(data, array = 1, columnProbe = "ControlType", probe = NULL,
  alpha = 0.5, size = 2)

Arguments

data	microarray data. Only for RGlist, MAlist or ELits class objects.
array	number array or name array to be displayed. Default 1.
columnProbe	column where contain probe number
probe	agilent type of probe. See in "ControlType" column. Default NULL, i.e. all.
alpha	transparent points (min = 1, max = 0). Default 0.25.
size	size of points. Default 2.

Details

An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values). If MA is an RGList or MAList then this function produces an ordinary within-array MA-plot. If MA is an MArrayLM object, then the plot is an fitted model MA-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis.

Value

A plot is created on the current graphics device.

AlexeiSleptcov/aggi documentation built on May 5, 2019, 4:53 a.m.