plot.pairwise.comparison: Plots a PairComp object
In simpleaffy: Very simple high level analysis of Affymetrix data

Description Usage Arguments Details Author(s) See Also Examples

Draws a scatter plot between means from a pairwise comparison. Colours according to PMA calls and identifies 'signficant' genes yielded by a filtering

1 2	## S3 method for class 'pairwise.comparison' plot(x,y=NULL,labels=colnames(means(x)),showPMA=TRUE,type="scatter",...)

`x`	A `PairComp` object
`y`	A `PairComp` object
`labels`	A list containing x and y axis labels
`showPMA`	True if PMA calls are to be identified
`type`	Can be 'scatter', 'ma' or 'volcano'
`...`	Additional arguments to plot

Takes a PairComp object (as produced by pairwise.comparison and plots a scatter plot between the sample means. If PMA calls are present in the calls slot of the object then it uses them to colour the points. Present on all arrays: red; absent on all arrays: yellow; present in all some arrays; orange. In addition, if a second PairComp object is supplied, it identifies spots in that object, by drawing them as black circles. This allows, for example, the results of a pairwise.filter to be plotted on the same graph.

If type is 'scatter' does a simple scatter plot. If type is 'volcano' does a volcano plot. If type is 'ma' does an MA plot.

Crispin J Miller

pairwise.comparison pairwise.filter trad.scatter.plot

  ## Not run: 
    pc <- pairwise.comparison(eset.mas,group="group",members=c("a","b"),spots=eset)
    pf <- pairwise.filter(pc)
    plot(pc,pf)
  
## End(Not run)