marrayInfo-class {marray} | R Documentation

## Class "marrayInfo", description of target samples or spotted probe sequences

### Description

This class is used to store information on target samples hybridized to a batch of arrays or probe sequences spotted onto these arrays. It is not specific to the microarray context.

### Objects from the Class

Objects can be created by calls of the form `new('marrayInfo',`
`maLabels = ...., # Object of class character`
`maInfo = ...., # Object of class data.frame`
`maNotes = ...., # Object of class character`
`)`

### Slots

`maLabels`:

  Object of class `"character"`, vector of spot or array labels.

`maInfo`:

  Object of class `"data.frame"`. If the object of class `"marrayInfo"` is used to describe probe sequences, rows of `maInfo` correspond to spots and columns to various gene identifiers and annotations. If the object of class `"marrayInfo"` is used to describe target samples hybridized to the arrays, rows of `maInfo` correspond to arrays and columns to various descriptions of the hybridizations, e.g., names of Cy3 and Cy5 samples, labels for the arrays etc.

`maNotes`:

  Object of class `"character"`, any notes on the target samples or spotted probe sequences.

### Methods

[

  `signature(x = "marrayInfo")`: subsetting operator for spots on the array or arrays in the batch, ensures that all slots are subset properly.

maGnames<-

  `signature(object = "marrayRaw", value = "marrayInfo")`: slot assignment method.

maGnames<-

  `signature(object = "marrayNorm", value = "marrayInfo")`: slot assignment method.

maGnames<-

  `signature(object = "marraySpots", value = "marrayInfo")`: slot assignment method.

maInfo

  `signature(object = "marrayInfo")`: slot accessor method.

maInfo<-

  `signature(object = "marrayInfo", value = "data.frame")`: slot assignment method.

maLabels

  `signature(object = "marrayInfo")`: slot accessor method.

maLabels<-

  `signature(object = "marrayInfo", value = "character")`: slot assignment method.

maLabels<-

  `signature(object = "marrayInfo", value = "numeric")`: slot assignment method.

maNotes

  `signature(object = "marrayInfo")`: slot accessor method.

maNotes<-

  `signature(object = "marrayInfo", value = "character")`: slot assignment method.

maTargets<-

  `signature(object = "marrayRaw", value = "marrayInfo")`: slot assignment method.

maTargets<-

  `signature(object = "marrayNorm", value = "marrayInfo")`: slot assignment method.

print

  `signature(x = "marrayInfo")`: print method for `"marrayInfo"` class.

### 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

`marrayLayout`, `marrayRaw`, `marrayNorm`.

### Examples

    ## See marrayRaw

[Package marray version 1.72.0 Index]