Object Oriented Microarray Library: Slide

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

Attributes

a

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

b

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

name

A character string describing this object.

Methods

slide(cs, aname, bname, ef, ...)

Constructor, given a complete slide object cs. The aname and bname arguments are optional character strings, which default to 'A' and 'B'. The optional ef argument is an extractor, with the default value of svol.extractor. Remaining arguments are passed along to the extractor.

transform(object, tf, ...)

Apply a common transform operation (tf) to both channels in a slide. Additional arguments are passed along to the transformer.

plot(object, ccl, ...)

Draw a scatter plot of the object. If the optional ccl argument is supplied as a list of color.coding objects, then the scatter plot will be plotted in different colors.

as.data.frame(object)

Returns a data frame containing the channel data in two columns labeled 'A' and 'B'.

summary(object, ...)

Write out a summary of the object.

print(object, ...)

Print all the information from the object.

image(object, name, ...)

Produces images of both channels. The optional name argument is used as a label.

Description

An object of the slide class represents a single kind of measurement performed at all spots on both channels of a complete slide object. Extracting the svol attributes, for example, produces a slide. So does extracting the background. So does a normalization procedure.

  x <- f.load.cg4.file('CG01180.txt', 'demo')
  s <- slide(x, ef=standard.channel)
  summary(s)
  plot(s)
  opar <- par(mfrow=c(2,1))
  image(s)
  par(opar)