Object Oriented Microarray Library: Within-Slide Replicates

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

Attributes

ra

An object of class cg4.replicate derived from the a channel of a complete slide.

rb

An object of class cg4.replicate derived from the b channel of a complete slide.

sa

An object of class single.group, obtained by scoring ra

.

sb

An object of class single.group, obtained by scoring rb

.

Methods

slide.replicate(cs, ef, ...)

Constructor. The first (required) argument is a complete.slide object. The optional ef argument is an extractor; it defaults to svol.extractor. The remaining arguments are passed along to the extractor.

plot(object, multiple, ccl, name, ...)

Produce a 2x2 grid of plots. The first one is a straight scatter plot of the replicates in the red channel. Next is a Baggerly-Coombes plot of the replicate intensities in the red channel. The optional multiple argument determines which multiple of the smoothed estimate of standard deviation is plotted; the default value is 3. The optional ccl argument allows the plot to be color-coded. The rmaining two plots are the same as the first two, except that they plot the replicates in the green channel.

Description

An object of the slide.replicate class corresponds to a quality control check on how well the replicate spots on a CG4 microarray behaved.