x should be an already configured cellHTS
object (state(x)["configured"]=TRUE), so that the information
about the well annotation of the plates is available.
The per-plate dynamic ranges are calculated for the data stored in
slot assayData of x. This can be raw data, normalized
data or scored data. If definition="difference", the dynamic range is calculated as
the absolute difference between the arithmetic average on positive and
negative controls.
If definition="ratio", the dynamic range is calculated as the
ratio between the geometric mean on positive and negative controls.
NOTE: the argument definition should only be set to
"ratio" if data are in positive scale!
If definition is missing it is determined based on the scale of
the data. By default, if data are in positive scale, definition is set
to "ratio", otherwise, it is set to "difference".
posControls and negControls should be given as a vector
of regular expression patterns specifying the name of the positive(s)
and negative(s) controls, respectivey, as provided in the plate
configuration file (and accessed via wellAnno(x)). The length
of these vectors should be equal to the current number of channels in
x (dim(Data(x))[3]). By default, if posControls
is not given, pos will be taken as the name for the wells
containing positive controls. Similarly, if negControls is
missing, by default neg will be considered as the name used to
annotated the negative controls. The content of posControls
and negControls will be passed to
regexpr for pattern matching within the
well annotation given in wellAnno(x) (see examples). If no
controls are available for a given channel, use "" or NA
for that channel. For example, posControls = c("",
"(?i)^diap$") means that channel 1 has no positive controls, while
diap is the positive control for channel 2.
The arguments posControls and negControls are
particularly useful in multi-channel data since the controls might be
reporter-specific, or after normalizing multi-channel data.
If there are different positive controls, the dynamic range is
calculated between each of the positive controls and the negative
controls.
In the case of a two-way assay, where two types of "positive" controls
are used in the screen ("activators" and "inhibitors"),
posControls should be defined as a list with two components
(called act and inh), each of which should be vectors of
regular expressions of the same length as the current number of
reporters (as explained above). The dynamic range is calculated
between each type of positive control (activators or
inhibitors) and the negative controls.