MmPalateMiRNA (version 1.22.0)

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, ...)


Either an RGList object, or a list containing MAList and/or NChannelSet objects
The channel to use for calculating distances, one of either "G" (green or control channel) or "R" (red or experimental channel)
An optional character string specifying the name of a factor to create separate panel displays, which must be in x$genes (for RGList objects)
An optional character vector specifying the which levels of 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 arrays together
arguments to pass to levelplot


signature(x = "RGList", data = "missing")
For RGList objects, separate panel displays can be produced for different types of probes, as determined by the group argument.
signature(x = "list", data = "missing")
The method for list objects is intended to work with lists of normalized data sets, as either MAList or NChannelSet objects. This method will produce separate panel displays for each normalized data set.


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.

See Also

densityplot for density plots of log2 intensity values, MADvsMedianPlot for median absolute deviation versus median plots, and MAplot for MA plots


Run this code
res <- levelplot(PalateData[, c(1,5,9,2:4,6:8)], 
                 channel="G", group="probe.type", 
                 subset=c("MMU miRNAs", "Other miRNAs", "Control", "Empty"), 
                 scales = list(rot=c(45, 45))) 

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