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

[Package marrayClasses version 1.2.9 Index]