marrayTwo-class {marrayClasses} | R Documentation

## Class "marrayTwo", classes and methods for microarray spot statistics

### Description

This class represents pre- or post-normalization intensity data for a batch of cDNA microarrays. A batch of arrays consists of a collection of arrays with the same layout (`"marrayLayout"`). The class contains slots for two types of spot statistics (e.g. the raw green (Cy3) and red (Cy5) foreground intensities, or normalized log-ratios M and average intensities A), the layout of the arrays, and a description of the target samples hybridized to the arrays

### Objects from the Class

Objects can be created by calls of the form `new('marrayRaw',`
`maX = ...., # Object of class matrix`
`maY = ...., # Object of class matrix`
`maLayout = ...., # Object of class marrayLayout`
`maTargets = ...., # Object of class marrayInfo`
`)`

### Slots

`maX`:
  Object of class `"matrix"`, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maY`:
  Object of class `"matrix"`, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maLayout`:
  Object of class `"marrayLayout"`, layout parameters for the cDNA microarrays.
`maTargets`:
  Object of class `"marrayInfo"`, description of target samples hybridized to the arrays.

### Methods

[
  `signature(x = "marrayTwo")`: subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
maControls
  `signature(object = "marrayTwo")`: slot accessor method.
maControls<-
  `signature(object = "marrayTwo")`: slot assignment method.
maGridCol
  `signature(object = "marrayTwo")`: method which computes a vector of grid column coordinates for each spot.
maGridRow
  `signature(object = "marrayTwo")`: method which computes a vector of grid row coordinates for each spot.
maLayout
  `signature(object = "marrayTwo")`: slot accessor method.
maLayout<-
  `signature(object = "marrayTwo", value = "marrayLayout")`: slot assignment method.
maNgc
  `signature(object = "marrayTwo")`: slot accessor method.
maNgc<-
  `signature(object = "marrayTwo", value = "numeric")`: slot assignment method.
maNgr
  `signature(object = "marrayTwo")`: slot accessor method.
maNgr<-
  `signature(object = "marrayTwo", value = "numeric")`: slot assignment method.
maNsamples
  `signature(object = "marrayTwo")`: slot accessor method.
maNsc
  `signature(object = "marrayTwo")`: slot accessor method.
maNsc<-
  `signature(object = "marrayTwo", value = "numeric")`: slot assignment method.
maNspots
  `signature(object = "marrayTwo")`: slot accessor method.
maNspots<-
  `signature(object = "marrayTwo", value = "numeric")`: slot assignment method.
maNsr
  `signature(object = "marrayTwo")`: slot accessor method.
maNsr<-
  `signature(object = "marrayTwo", value = "numeric")`: slot assignment method.
maPlate
  `signature(object = "marrayTwo")`: slot accessor method.
maPlate<-
  `signature(object = "marrayTwo")`: slot assignment method.
maPrintTip
  `signature(object = "marrayTwo")`: method which computes a vector of print-tip-group indices for each spot.
maSpotCol
  `signature(object = "marrayTwo")`: method which computes a vector of spot column coordinates for each spot.
maSpotRow
  `signature(object = "marrayTwo")`: method which computes a vector of spot row coordinates for each spot.
maSub
  `signature(object = "marrayTwo")`: slot accessor method.
maSub<-
  `signature(object = "marrayTwo")`: slot assignment method.
maTargets
  `signature(object = "marrayTwo")`: slot accessor method.
maTargets<-
  `signature(object = "marrayTwo", value = "marrayInfo")`: slot assignment method.
maX
  `signature(object = "marrayTwo")`: slot accessor method.
maX<-
  `signature(object = "marrayTwo", value = "matrix")`: slot assignment method.
maY
  `signature(object = "marrayTwo")`: slot accessor method.
maY<-
  `signature(object = "marrayTwo", value = "matrix")`: slot assignment method.
print
  `signature(x = "marrayTwo")`: print method for `"marrayTwo"` class.

### Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.

### 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`, `marrayInfo`, `marraySpots`, `print-methods`, `[-methods`.

### Examples

    ## See marrayRaw

[Package Contents]