levelplot: Pairwise distance between arrays
Calculates and plots the pairwise distance between arrays, as measured
by the median of the absolute differences in log2 intensity values.
"levelplot"( x, channel=c("G", "R"), group=NULL, subset=NULL, ...)
"levelplot"( x, channel=c("G", "R"), order=NULL, ...)
The channel to use for calculating distances, one of
either "G" (green or control channel) or "R" (red or experimental
An optional character string specifying the name of a
factor to create separate panel displays, which must be in
An optional character vector specifying the which levels
group to use in creating separate panel displays
An optional numeric vector specifying the order of the
arrays to use in producing the distance plots, i.e. for grouping certain
signature(x = "RGList", data = "missing")
RGList objects, separate panel
can be produced for different types of probes, as determined by the
signature(x = "list", data = "missing")
The method for
list objects is intended
to work with lists of normalized data sets, as either
NChannelSet objects. This
method will produce separate panel displays for each normalized data
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin,
C. Drescher, W. Huber, R. Gentleman, and M. Tewari.
Quality assessment and data analysis for microRNA expression arrays.
Nucleic Acids Res, 37(2):e17, 2009.
res <- levelplot(PalateData[, c(1,5,9,2:4,6:8)],
subset=c("MMU miRNAs", "Other miRNAs", "Control", "Empty"),
scales = list(rot=c(45, 45)))