marraySpots-class {marrayClasses} | R Documentation

## Class "marraySpots", classes and methods for probe sequences spotted on microarrays

### Description

This class stores information on the spotted probe sequences for a batch of arrays. A batch of arrays consists of a collection of arrays with the same layout (`"marrayLayout"`). The class contains slots for the layout of the arrays, and a description of the probe sequences spotted onto the arrays.

### Objects from the Class

Objects can be created by calls of the form `new('marraySpots',`
`maGnames = ...., # Object of class marrayInfo`
`maLayout = ...., # Object of class marrayLayout`

### Slots

`maGnames`:
  Object of class `"marrayInfo"`, description of spotted probe sequences.
`maLayout`:
  Object of class `"marrayLayout"`, layout parameters for the cDNA microarrays.

### Methods

[
  `signature(x = "marraySpots")`: subsetting operator for spots on the array, ensures that all slots are subset properly.
coerce
  `signature(from = "marrayRaw", to = "marraySpots")`: coerce an object of class `"marrayRaw"` into an object of class `"marraySpots"`.
coerce
  `signature(from = "marrayNorm", to = "marraySpots")`: coerce an object of class `"marrayNorm"` into an object of class `"marraySpots"`.
maControls
  `signature(object = "marraySpots")`: slot accessor method.
maControls<-
  `signature(object = "marraySpots")`: slot assignment method.
maGnames
  `signature(object = "marraySpots")`: slot accessor method.
maGnames<-
  `signature(object = "marraySpots", value = "marrayInfo")`: slot assignment method.
maGridCol
  `signature(object = "marraySpots")`: method which computes a vector of grid column coordinates for each spot.
maGridRow
  `signature(object = "marraySpots")`: method which computes a vector of grid row coordinates for each spot.
maLayout
  `signature(object = "marraySpots")`: slot accessor method.
maLayout<-
  `signature(object = "marraySpots", value = "marrayLayout")`: slot assignment method.
maNgc
  `signature(object = "marraySpots")`: slot accessor method.
maNgc<-
  `signature(object = "marraySpots", value = "numeric")`: slot assignment method.
maNgr
  `signature(object = "marraySpots")`: slot accessor method.
maNgr<-
  `signature(object = "marraySpots", value = "numeric")`: slot assignment method.
maNsc
  `signature(object = "marraySpots")`: slot accessor method.
maNsc<-
  `signature(object = "marraySpots", value = "numeric")`: slot assignment method.
maNspots
  `signature(object = "marraySpots")`: slot accessor method.
maNspots<-
  `signature(object = "marraySpots", value = "numeric")`: slot assignment method.
maNsr
  `signature(object = "marraySpots")`: slot accessor method.
maNsr<-
  `signature(object = "marraySpots", value = "numeric")`: slot assignment method.
maPlate
  `signature(object = "marraySpots")`: slot accessor method.
maPlate<-
  `signature(object = "marraySpots")`: slot assignment method.
maPrintTip
  `signature(object = "marraySpots")`: method which computes a vector of print-tip-group indices for each spot.
maSpotCol
  `signature(object = "marraySpots")`: method which computes a vector of spot column coordinates for each spot.
maSpotRow
  `signature(object = "marraySpots")`: method which computes a vector of spot row coordinates for each spot.
maSub
  `signature(object = "marraySpots")`: slot accessor method.
maSub<-
  `signature(object = "marraySpots")`: slot assignment method.
print
  `signature(x = "marraySpots")`: print method for `"marraySpots"` 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`, `marrayTwo`, `print-methods`, `[-methods`.

### Examples

    ## See marrayRaw

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