Object Oriented Microarray Library: Complete Slide

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

Attributes

a

A complete channel object, usually representing the red (Cy5) channel.

b

A complete channel object, usually representing the green (Cy3) channel.

name

A character string describing this object.

Constructors

complete.slide(a, b, name)

Creates a complete slide from two complete channels (a and b) and a character string (name).

f.load.cg4.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. The constructor has been used on the core lab amplification data set.

f.load.cg4(listing, root)

Alternate constructor. This takes an argument listing that contains attributes filename and varname. The latter is used both as the target of an assignment as well as the internal name of the object. The optional root argument is a character string containing a directory name. It defaults to the empty string. If you supply one, then it must terminate with a forward slash.

f.load.cg8.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. The constructor has been used on the core lab amplification data set.

f.load.cg8(listing, root)

Alternate constructor. This takes an argument listing that contains attributes filename and varname. The latter is used both as the target of an assignment as well as the internal name of the object. The optional root argument is a character string containing a directory name. It defaults to the empty string. If you supply one, then it must terminate with a forward slash.

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

Another constructor, resulting from a different protocol that stored different fields in the ArrayVision file.

f.load.latha(listing, root)

Alternate form of constructor; see f.load.cg4.

Methods

as.data.frame(object, ...)

Collect the data from both channels into a single data frame.

print(object, ...)

Print all the information from the object.

summary(object, ...)

Write out a summary of the object.

plot(object, name, uselog)

The plot method estimates and graphs the estimated probability density functions for the six vectors guaranteed to belong to a complete.slide. The optional name argument is used as a label. The optional uselog determines whether the data is log-transformed first; the default value is false.

image(object, name, uselog, ef, ...)

Produce corresponding images for the two complete channels. The optional name argument is used as a label. The optional uselog argument determines whether or not the data is log-transformed; the default value is false. The optional ef argument is an extractor function; the default value is bkgd.extractor. Any additional arguments are passed along to the extractor.

analyze(object, name, which, ...)

Perform the complete basic analysis of this object. The optional name argument is used as a label. The optional which argument is an extractor; its default value is standard.channel. All remaining arguments are passed along to the extractor.

evaluate.background(object, thresh, name)

This method compares the estimated background values with the standard normalization procedure after thresholding at the given level.

Description

An object of the complete.slide class represents a single glass microarray used in a two-color fluorescence experiment. The typical way to construct such an object is to read in a file that was produced in ArrayVision. You can quickly generate a large number of graphs (as part of our basic analysis) just by applying the analyze method.

  x <- f.load.cg4.file('CG01180.txt', 'demo')
  summary(x)
  plot(x)
  evaluate.background(x)
  opar <- par(mfrow=c(2,1))
  image(x)
  image(x, ef=svol.extractor)
  par(opar)