Pairwise distance between arrays

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Description

Calculates and plots the pairwise distance between arrays, as measured by the median of the absolute differences in log2 intensity values.

Usage

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## S4 method for signature 'RGList,missing'
levelplot(
    x,
    channel=c("G", "R"),
    group=NULL,
    subset=NULL, 
    ...)

## S4 method for signature 'list,missing'
levelplot(
    x,
    channel=c("G", "R"),
    order=NULL, 
    ...)

Arguments

x

Either an RGList object, or a list containing MAList and/or NChannelSet objects

channel

The channel to use for calculating distances, one of either "G" (green or control channel) or "R" (red or experimental channel)

group

An optional character string specifying the name of a factor to create separate panel displays, which must be in x$genes (for RGList objects)

subset

An optional character vector specifying the which levels of group to use in creating separate panel displays

order

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

Methods

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.

References

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

Examples

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data(PalateData)
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))) 
print(res)