densityplot {MmPalateMiRNA} | R Documentation

## Density plots of log2 intensity values

### Description

Plots the estimated density of log2 intensity values for two-color microarrays

### Usage

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

    ## S4 method for signature 'list,missing'
    densityplot(
        x,
        channel=c("G", "R"),
        group=NULL,
        subset=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
`...` | arguments to pass to `densityplot`

### 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, additionally subsetted by the `group` argument if supplied. The `useOuterStrips` function in the latticeExtra package can be used for ‘outer’ strip labels in the latter case.

### 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

`levelplot` for pairwise distance plots between arrays, `MADvsMedianPlot` for median absolute deviation versus median plots, and `MAplot` for MA plots

### Examples

    data(PalateData)
    res <- densityplot(PalateData, channel="G", group="probe.type",
                       subset = c("Other miRNAs",   "MMU miRNAs", "Control"),
                       col=rep(1:3, each=3), lty=rep(1:3, 3),
                       key = list(lines=list(col=rep(1:3, each=3), lty=rep(1:3, 3)),
                         columns=3))
    print(res)

[Package MmPalateMiRNA version 1.30.0 Index]