pairs.AffyBatch {affy}R Documentation

plot intensities using 'pairs'


Plot intensities using the function 'pairs'


  pairs.AffyBatch(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)


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


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'.


[Package affy version 1.8.1 Index]