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plotFB

FB-Plot


Description

Creates foreground-background plots.

Usage

## S3 method for class 'RGList'
plotFB(x, array = 1, lim = "separate", pch = 16, cex = 0.3,
     xlab = "log2 Background", ylab = "log2 Foreground", main = colnames(x)[array], ...)
## S3 method for class 'EListRaw'
plotFB(x, array = 1, pch = 16, cex=0.3,
     xlab = "log2 Background", ylab = "log2 Foreground", main = colnames(x)[array], ...)

Arguments

x

an RGList or EListRaw object.

array

integer giving the array to be plotted.

lim

character string indicating whether the red and green plots should have "separate" or "common" x- and y- co-ordinate limits.

pch

vector or list of plotting characters. Defaults to integer code 16.

cex

numeric vector of plot symbol expansions.

xlab

character string, label for x-axis.

ylab

character string, label for y-axis.

main

character string, title for plot.

...

any other arguments are passed to plot.

Details

A foreground-background plot is a plot of log2-foreground vs log2-background for a particular array. For two-color arrays, this function produces a pair of plots, one for the green channel and one for the red.

See points for possible values for pch, col and cex.

Value

A plot is created on the current graphics device.

Author(s)

Gordon Smyth

See Also

An overview of diagnostic functions available in LIMMA is given in 09.Diagnostics.


limma

Linear Models for Microarray Data

v3.46.0
GPL (>=2)
Authors
Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]
Initial release
2020-10-19

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