Boxplot for observed (log-)intensities in a FeatureSet-like object
(ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet,
TilingFeatureSet) and ExpressionSet.
character defining what probe types are to be used in the
plot.
transfo
a function to transform the data before plotting. See
'Details'.
nsample
number of units to sample and build the plot.
...
arguments to be passed to the default boxplot method.
Details
The 'transfo' argument will set the transformation to be used. For raw
data, 'transfo=log2' is a common practice. For summarized data (which
are often in log2-scale), no transformation is needed (therefore 'transfo=identity').
Note
The boxplot methods for FeatureSet and Expression use a
sample (via sample) of the probes/probesets to produce the
plot. Therefore, the user interested in reproducibility is advised to
use set.seed.