marrayNorm-class {marrayClasses} | R Documentation |
This class represents 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 the average log-intensities A, the normalized log-ratios M, the location and scale normalization values, the layout of the arrays, and descriptions of the target samples hybridized to the arrays and probe sequences spotted onto the arrays.
Objects can be created by calls of the form
new('marrayNorm',
maA = ...., # Object of class matrix
maM = ...., # Object of class matrix
maMloc = ...., # Object of class matrix
maMscale = ...., # Object of class matrix
maW = ...., # Object of class matrix
maLayout = ...., # Object of class marrayLayout
maGnames = ...., # Object of class marrayInfo
maTargets = ...., # Object of class marrayInfo
maNotes = ...., # Object of class character
maNormCall = ...., # Object of class call
)
maA
:"matrix"
, average log-intensities (base 2) A, rows correspond to spotted probe sequences, columns to arrays in the batch.maM
:"matrix"
, intensity log-ratios (base 2) M, rows correspond to spotted probe sequences, columns to arrays in the batch.maMloc
:"matrix"
, location normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.maMscale
:"matrix"
, scale normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.maW
:"matrix"
, spot quality weights, rows correspond to spotted probe sequences, columns to arrays in the batch.maLayout
:"marrayLayout"
, layout parameters for cDNA microarrays.maGnames
:"marrayInfo"
, description of spotted probe sequences.maTargets
:"marrayInfo"
, description of target samples hybridized to the arrays.maNotes
:"character"
, any notes concerning the microarray experiments, e.g. hybridization or scanning conditions.maNormCall
:"call"
, function call for normalizing the batch of arrays.signature(x = "marrayNorm")
: subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.signature(from = "marrayRaw", to = "marrayNorm")
: coerce an object of class "marrayRaw"
into an object of class marrayNorm
. signature(from = "marrayNorm", to = "exprSet")
: coerce an object of class "marrayNorm"
into an object of class exprSet-class
. signature(from = "marrayNorm", to = "marraySpots")
: coerce an object of class "marrayNorm"
into an object of class "marraySpots"
. signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "matrix")
: slot assignment method.signature(object = "marrayNorm")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "marrayInfo")
: slot assignment method.signature(object = "marrayNorm")
: method which computes a vector of grid column coordinates for each spot.signature(object = "marrayNorm")
: method which computes a vector of grid row coordinates for each spot.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "marrayLayout")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "matrix")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "matrix")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "matrix")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "numeric")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "numeric")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "character")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "numeric")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "numeric")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "numeric")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm")
: slot assignment method.signature(object = "marrayNorm")
: method which computes a vector of print-tip-group indices for each spot.signature(object = "marrayNorm")
: method which computes a vector of spot column coordinates for each spot.signature(object = "marrayNorm")
: method which computes a vector of spot row coordinates for each spot.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "marrayInfo")
: slot assignment method.signature(object = "marrayNorm")
: slot accessor method.signature(object = "marrayNorm", value = "matrix")
: slot assignment method.signature(x = "marrayNorm")
: print method for "marrayNorm"
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
, marrayInfo
, marraySpots
, marrayTwo
, exprSet-class
, print-methods
, [-methods
, coerce-methods
.
# Examples use swirl dataset, for description type ? swirl # data(swirl) # Normalization is done using functions from the marrayNorm package # library(marrayNorm) # Within-print-tip-group loess location normalization # mnorm<-maNorm(swirl[,2:3],norm="p") # Object of class marrayNorm for the second and third swirl arrays # mnorm # Function call # maNormCall(mnorm) # Object of class marrayInfo -- Probe sequences # maGnames(mnorm) # Object of class marrayInfo -- Target samples # maTargets(mnorm) # Density plot of log-ratios M for third array # plot(density(maM(mnorm[,2])), lwd=2, col=2, main="Density plots of log-ratios M") # lines(density(maM(swirl[,3])), lwd=2) # abline(v=0) # legend(2,1,c("Pre-normalization","Post-normalization"))