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 horizonal axis
`M` | A vector to plot along vertical axis
`subset` | A set of indices to use when drawing the loess curve
`show.statistics` | 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

       data(affybatch.example)
       MAplot(affybatch.example)
       Mbox(affybatch.example)

[Package affy version 1.18.2 Index]