levelplot {MmPalateMiRNA} | R Documentation

## Pairwise distance between arrays

### Description

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

### Usage

    ## 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

    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)

[Package MmPalateMiRNA version 1.30.0 Index]