Object Oriented Microarray Library: Complete Channel

The complete channel module provides the definition of the complete.channel class. See the bottom of the page for an example of how the class can be used.

Requirements

This class uses the channel type package, which must be loaded in order for the routines in this package to work correctly.

Attributes

name

A character string: the name of this experimental channel.

type

The type of array and labeling; this is an object of class channel.type.

data

This is a data.frame, typically read from a quantification file produced by ArrayVision. It is guaranteed to at least contain columns named vol, bkgd, and svol.

Constructors

f.load.clontech.file(filename, name)

Constructor, which takes the name of an ArrayVision file along with a name that will be used as a label for this object. This constructor has been used on the Huff data set, which used the Clontech ATLAS Human Cancer 1.2 arrays.

f.load.clontech(listing, root)

Alternate constructor. This takes an argument listing that contains attributes called filename, which describes the source of the data, and varname, which is used both as the target of an assignment and as the internal name component. The optional root argument is a character string describing the directory in which the files are stored. It defaults to the empty string. If you supply an argument, it must terminate with a forward slash.

f.load.gf.vertical.file(filename, name)

Constructor, which takes the name of an ArrayVision file along with a name that will be used as a label for this object. This constructor has been used on the Abruzzo data set, which uses Research Genetics GeneFilter arrays, models GF200 through GF205, quantified with the barcode at the bottom.

f.load.gf.vertical(listing, root)

Alternate constructor; see f.load.clontech.

f.load.gf.horizontal.file(filename, name)

Constructor, which takes the name of an ArrayVision file along with a name that will be used as a label for this object. This constructor has been used on the McDonnell data set, which uses Research Genetics GeneFilter arrays, models GF200 through GF205, quantified with the barcode on the right side.

f.load.gf.horizontal(listing, root)

Alternate constructor; see f.load.clontech.

Methods

as.data.frame(object)

Convert the object into a data frame by returning its data component.

print(object,...)

Print all the data for this object.

summary(object, ...)

Write out a short summary of the object.

plot(object, name=object$name, uselog=F, ...)

The plotting routine generates graphs of the estimated probability density functions of the three data components (vol, bkgd, and svol) of the object. The optional name argument will override the internal name as part of the main title on the plot. The optional logical argument uselog determines whether or not the data is log-transformed before estimating the density functions.

analyze(object, uselog=F)

This method computes the estimated probability density functions for the three data components, and returns them as a list.

image(object, ...)

Uses the image method for channel objects to produce geographically aligned images of the log-transformed intensity and background estimates.

Description

An object of the complete.channel class represents one channel (red or green) of a two-color fluorescence microarray experiment. Alternatively, it can also represent the entirety of a radioactive microarray experiment. The constructors described here read in ArrayVision files from single channel radioactive isotope experiments. To construct complete channels from the raw data of a fluorescence experiment, you must first read in the combined data file to produce a complete.slide object.

  x <- f.load.clontech.file('/huff/05082000a-4.txt', 'Wild4')

  summary(x)

  opar <- par(mfrow=c(2,3))
  plot(x)
  plot(x, name='whatever', uselog=T)
  par(opar)