plotMA {beadarray} | R Documentation |
Function which produces an MA plot between two specified arrays.
plotMA(exprs, array1=1, array2=2, genesToLabel=NULL, labelCol="red", foldLine=2, log=TRUE, labelpch=16, ma.ylim=2, sampleSize=NULL,...)
exprs |
a matrix of expression values |
array1 |
integer specifying the first array to plot |
array2 |
integer specifying the second array to plot |
genesToLabel |
vector of genes to highlight on the plot.
These must match the rownames of exprs . |
labelCol |
plotting colours for highlighted genes |
foldLine |
a numeric value defining where to draw horizontal fold-change lines on the plot |
log |
if TRUE the data will be log-transformed before plotting |
labelpch |
plotting characters for highlighted genes |
ma.ylim |
numeric value specifying the range of the plot (from -ma.ylim to ma.ylim) |
sampleSize |
The number of genes to plot. Default is NULL, which plots every gene. |
... |
other graphical parameters to plot that can be specified |
The log2 difference in intensity (M-value, log-ratio) are plotted against the log2 average intensity (A-value) for each probe for the two arrays selected.
A smoothed MA scatter plot is displayed on the current graphical device.
Mark Dunning
data(BSData) plotMA(exprs(BSData), array1=1, array2=2)