boxplot {marray} | R Documentation |

## Boxplots for cDNA microarray spot statistics

### Description

The function `boxplot`

produces boxplots of microarray spot
statistics for the classes `"marrayRaw"`

,
`"marrayNorm"`

.
We encourage users to use `boxplot`

rather than `maBoxplot`

.
The name of the arguments have changed slightly.

### Usage

## S4 method for signature 'marrayRaw':
boxplot(x, xvar="maPrintTip", yvar="maM", ...)
## S4 method for signature 'marrayNorm':
boxplot(x, xvar="maPrintTip", yvar="maM", ...)

### Arguments

`x` |
Microarray object of class `"marrayRaw"` , `"marrayNorm"` |

`xvar` |
Name of accessor method for the spot statistic used to
stratify the data, typically a slot name for the microarray layout
object (see `"marrayLayout"` ) such as `maPlate` or
a method such as `maPrintTip` . If `x` is NULL, the data
are not stratified. |

`yvar` |
Name of accessor method for the spot statistic of
interest, typically a slot name for the microarray object `m` ,
such as `maM` . |

`...` |
Optional graphical parameters, see `par` . |

### Details

If there are more than one array in the batch, the function produces a
boxplot for each array in the batch. Such plots are useful when
assessing the need for between array normalization, for example, to deal
with scale differences among different arrays. Default graphical
parameters are chosen for convenience using the function
`maDefaultPar`

(e.g. color palette, axis labels, plot
title) but the user has the option to overwrite these parameters at any
point.

### Author(s)

Jean Yang and Sandrine Dudoit

### References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
exploratory analysis and normalization of cDNA microarray data. In
G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors,
*The Analysis of Gene Expression Data: Methods and Software*,
Springer, New York.

### See Also

`maBoxplot`

, `maDefaultPar`

.

### Examples

# To see the demo type demo(marrayPlots)
# Examples use swirl dataset, for description type ? swirl
data(swirl)
# Boxplots of pre-normalization log-ratios M for each of the 16
# print-tip-groups for the Swirl 93 array.
# - Default arguments
boxplot(swirl[,3])
# All spots
boxplot(swirl[,3], xvar=NULL, col="green")
# Boxplots of pre-normalization red foreground intensities for each grid row
# for the Swirl 81 array.
boxplot(swirl[,1], xvar="maGridRow", yvar = "maRf", main = "Swirl array 81: pre-normalization red foreground intensity")
# Boxplots of pre-normalization log-ratios for each array in swirl
boxplot(swirl, main="Swirl arrays: pre-normalization log-ratios")

[Package

*marray* version 1.8.0

Index]