MAplot {MmPalateMiRNA} | R Documentation

## MA plot

### Description

Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.

### Usage

    MAplot(x, ...)

    ## S4 method for signature 'MAList'
    MAplot(
        x,
        ...)

    ## S4 method for signature 'NChannelSet'
    MAplot(
        x,
        ...)

### Arguments

`x` | Either an `MAList` object or an `NChannelSet` object
`...` | arguments to pass to `xyplot`

### Details

The so-called "MA" plot can be used to evaluate whether their is a bias associated with overall intenstity level for each array. Loess smoothed regression lines are superimposed on each plot to demonstrate the trend.

### Methods

`signature(x = "MAList")`

  `M` and `A` values are stored as matrices in `x`

`signature(x = "NChannelSet")`

  `M` and `A` values are calculated from the `R` and `G` matrices returned by `assayData(x)`

### See Also

`densityplot` for density plots of log2 intensity values, `levelplot` for pairwise distance plots between arrays, and `MADvsMedianPlot` for median absolute deviation versus median plots.

### Examples

    data(PalateData)
    reducedSet <- filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"),
                              frac=1.1, number=3, reps=4)
    ndata.quantile <- normalizeBetweenArrays(reducedSet, method="quantile")
    res <- MAplot(ndata.quantile)
    print(res)

[Package MmPalateMiRNA version 1.36.0 Index]