marrayNorm-class {marray} | 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`.

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`

### Examples

    # Examples use swirl dataset, for description type ? swirl

    data(swirl)

    # Median normalization
    mnorm<-maNorm(swirl[,2:3],norm="m")

    # 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 marray version 1.70.0 Index]