RLEPlot
generates three different types of
relative log expression plots for highdimensional data.
1 2 3 
X 
A matrix of gene expression values. 
Y 
A matrix of gene expression values. 
center 
A logical scalar; 
name 
A vector of characters describing the data contained in

title 
A character string describing the title of the plot. 
method 
The type of RLE plot to be displayed; possible inputs are

anno 
A dataframe or a matrix containing the annotation of
arrays in 
Factor 
A character string corresponding to a column name of

numeric 
A logical scalar indicating whether 
new.legend 
A vector describing the names used for labelling; if 
outlier 
A logical indicating whether outliers should be plotted; only
applicable when 
There are three different RLE plots that can be generated using RLEPlot
:
"IQR.points"
Median expression vs. interquantile range of every array.
"IQR.boxplots"
Boxplots of the 25% and 75% quantile of all arrays.
"Minmax"
Ordinary RLE plots for the 5 arrays with the smallest and largest interquantile ranges.
Note that normal RLE plots are not supplied as they are not very suitable for highdimensional data.
RLEPlot
returns a plot.
Saskia Freytag, Terry Speed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  Y<simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1,
250, 100, intercept=FALSE, check.input=FALSE)
Y.hat<RUVNaiveRidge(Y, center=TRUE, nc_index=251:500, 0, 10, check.input=TRUE)
try(dev.off(), silent=TRUE)
par(mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.points")
try(dev.off(), silent=TRUE)
par(mfrow=c(1, 1))
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.boxplots")
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="minmax")
#Create a random annotation file
anno<as.matrix(sample(1:4, dim(Y.hat)[1], replace=TRUE))
colnames(anno)<"Factor"
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.points",
anno=anno, Factor="Factor", numeric=TRUE)

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