type of border elements to be used, one of “pos”, “neg”, or both.
qualopt
character string specifying whether to draw boxplots for “raw”,
“adjusted”, or “normalized” border intensities.
radius
determines the radius within which the COI for each array should be located.
linecol
the color of the ablines and the circle to be drawn.
visible
logical, if TRUE then arrays outside the circle with radius will be
flagged by labeling the data point with the array name.
...
optional arguments to be passed to coiplot.
Value
The names ot the outlier arrays, otherwise NULL.
Details
Produces Center-Of-Intensity (COI) plot(s) of the positive and negative feature intensities for
an object of class QualTreeSet. This plot is useful for detecting spatial biases
in intensities on an array.
Mean intensities for the left, right, top and bottom border elements are calculated, separated
into positive and negative controls, and the “center of intensity” is calculated on a
relative scale [-1,1]. Arrays with a COI outside a range with radius are considered to
be outliers. If visible = TRUE then outlier arrays will be flagged by labeling the data
point(s) with the array name(s).
## Not run: # ## border intensities, created by e.g. rmaPLM()# coiplot(rlm.all)# coiplot(rlm.all, type="pos")# coiplot(rlm.all, type="neg", radius=0.1)# ## End(Not run)