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 marrayClasses version 1.2.9 Index]