# MAplot: Relative M vs. A plots In affy: Methods for Affymetrix Oligonucleotide Arrays

## 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

 ```1 2 3 4 5 6``` ```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.

`mva.pairs`

## Examples

 ```1 2 3 4 5``` ```if (require(affydata)) { data(Dilution) MAplot(Dilution) Mbox(Dilution) } ```

### Example output

```Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

The following objects are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

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