marrayNorm-class {marrayClasses} | R Documentation

## Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data

### Description

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 from the Class

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`
`)`

### Slots

`maA`:
  Object of class `"matrix"`, average log-intensities (base 2) A, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maM`:
  Object of class `"matrix"`, intensity log-ratios (base 2) M, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maMloc`:
  Object of class `"matrix"`, location normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maMscale`:
  Object of class `"matrix"`, scale normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maW`:
  Object of class `"matrix"`, spot quality weights, rows correspond to spotted probe sequences, columns to arrays in the batch.
`maLayout`:
  Object of class `"marrayLayout"`, layout parameters for cDNA microarrays.
`maGnames`:
  Object of class `"marrayInfo"`, description of spotted probe sequences.
`maTargets`:
  Object of class `"marrayInfo"`, description of target samples hybridized to the arrays.
`maNotes`:
  Object of class `"character"`, any notes concerning the microarray experiments, e.g. hybridization or scanning conditions.
`maNormCall`:
  Object of class `"call"`, function call for normalizing the batch of arrays.

### Methods

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

### Examples

    # 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"))

[Package Contents]