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affy (version 1.50.0)

pairs.AffyBatch: plot intensities using 'pairs'

Description

Plot intensities using the function 'pairs'

Usage

"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'.