plotMA {beadarray} | R Documentation |
Function to show an MA plot between two specified samples from different BeadArrays.
plotMA(exprs, array1=1, array2=2, genesToLabel=NULL, labelCol="red", foldLine=2, log=TRUE, labelpch=16, ma.ylim=2, sampleSize=NULL,...)
exprs |
expression matrix from an ExpressionSet or eSet |
array1 |
numeric value to specify the first sample to be plotted |
array2 |
numeric value to specify the second sample to be plotted (optional) |
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 |
On the y axis, the log-2 difference in intensity (M-values) between the two samples is shown and along the x axis, the log-2 average intensity (A-values) are plotted.
MA plot is displayed on current graphical device.
Mark Dunning
data(BSData) plotMA(exprs(BSData), array1=1, array2=2)