marrayTwo-class {marrayClasses} | R Documentation |
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 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
)
maX
:"matrix"
, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.maY
:"matrix"
, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.maLayout
:"marrayLayout"
, layout parameters for the cDNA microarrays.maTargets
:"marrayInfo"
, description of target samples hybridized to the arrays.signature(x = "marrayTwo")
: subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo")
: slot assignment method.signature(object = "marrayTwo")
: method which computes a vector of grid column coordinates for each spot.signature(object = "marrayTwo")
: method which computes a vector of grid row coordinates for each spot.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "marrayLayout")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "numeric")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "numeric")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "numeric")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "numeric")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "numeric")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo")
: slot assignment method. signature(object = "marrayTwo")
: method which computes a vector of print-tip-group indices for each spot.signature(object = "marrayTwo")
: method which computes a vector of spot column coordinates for each spot.signature(object = "marrayTwo")
: method which computes a vector of spot row coordinates for each spot.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "marrayInfo")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "matrix")
: slot assignment method.signature(object = "marrayTwo")
: slot accessor method.signature(object = "marrayTwo", value = "matrix")
: slot assignment method.signature(x = "marrayTwo")
: print method for "marrayTwo"
class.Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
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.
marrayLayout
, marrayRaw
, marrayNorm
, marrayInfo
, marraySpots
, print-methods
, [-methods
.
## See marrayRaw