MAplot {affy} | R Documentation

## Relative M vs. A plots

### Description

Create boxplots of M or M vs A plots. Where M is determined relative to a specified chip or to a pseudo-median reference chip.

### Usage

    MAplot(object,...)
    Mbox(object,...)
    ma.plot(A, M, subset = sample(1:length(M), min(c(10000, length(M)))),
            show.statistics = TRUE, span = 2/3, family.loess = "gaussian",
            cex = 2, plot.method = c("normal","smoothScatter","add"),
            add.loess = TRUE, lwd = 1, lty = 1, loess.col = "red", ...)

### Arguments

`object` | an `AffyBatch-class`.
`...` | additional parameters for the routine.
`A` | a vector to plot along the horizontal axis.
`M` | a vector to plot along vertical axis.
`subset` | a set of indices to use when drawing the loess curve.
`show.statistics` | logical. If TRUE, some summary statistics of the M values are drawn.
`span` | span to be used for loess fit.
`family.loess` | `"guassian"` or `"symmetric"` as in `loess`.
`cex` | size of text when writing summary statistics on plot.
`plot.method` | a string specifying how the plot is to be drawn. `"normal"` plots points, `"smoothScatter"` uses the `smoothScatter` function. Specifying `"add"` means that the MAplot should be added to the current plot.
`add.loess` | add a loess line to the plot.
`lwd` | width of loess line.
`lty` | line type for loess line.
`loess.col` | color for loess line.

### See Also

`mva.pairs`

### Examples

    if (require(affydata)) {
       data(Dilution)
       MAplot(Dilution)
       Mbox(Dilution)
    }

[Package affy version 1.68.0 Index]