plot intensities using 'pairs'

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Description

Plot intensities using the function 'pairs'

Usage

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## S3 method for class 'AffyBatch'
pairs(x, panel=points, ..., transfo=I, main=NULL, oma=NULL,
                  font.main = par("font.main"),
                  cex.main = par("cex.main"), cex.labels = NULL, 
                  lower.panel=panel, upper.panel=NULL, diag.panel=NULL,
                  font.labels = 1, row1attop = TRUE, gap = 1)

Arguments

x

an AffyBatch object.

panel

a function to produce a plot (see pairs).

...

extra parameters for the 'panel' function.

transfo

a function to transform the intensity values before generating the plot. 'log' and 'log2' are popular choices.

main

title for the plot

oma

see 'oma' in par.

font.main

see pairs.

cex.main

see pairs.

cex.labels

see pairs.

lower.panel

a function to produce the plots in the lower triangle (see pairs).

upper.panel

a function to produce the plots in the upper triangle (see pairs).

diag.panel

a function to produce the plots in the diagonal (see pairs).

font.labels

see pairs.

row1attop

see pairs.

gap

see pairs.

Details

Plots with several chips can represent zillions of points. They require a lot of memory and can be very slow to be displayed. You may want to try to split of the plots, or to plot them in a device like 'png' or 'jpeg'.

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