This package defines the following data classes.
RGList
read.maimages
.
MAList
RGList
using MA.RG
or normalizeWithinArrays
.
Objects of this class contain one row for each spot.
There may be more than one spot and therefore more than one row for each probe.
EListRaw
read.maimages
.
EList
normalizeBetweenArrays
.
MArrayLM
lmFit
.
Objects of this class normally contain only one row for each unique probe.
TestResults
decideTests
.
Objects of this class normally contain one row for each unique probe.
All these data classes obey many analogies with matrices.
In the case of RGList
, MAList
, EListRaw
and EList
, rows correspond to spots or probes and columns to arrays.
In the case of MarrayLM
, rows correspond to unique probes and the columns to parameters or contrasts.
The functions summary
, dim
, length
, ncol
, nrow
, dimnames
, rownames
, colnames
have methods for these classes.
Objects of any of these classes may be subsetted.
Multiple data objects may be combined by rows (to add extra probes) or by columns (to add extra arrays).
Furthermore all of these classes may be coerced to actually be of class matrix
using as.matrix
, although this entails loss of information.
Fitted model objects of class MArrayLM
can be coerced to class data.frame
using as.data.frame
.
The first three classes belong to the virtual class LargeDataObject
.
A show
method is defined for LargeDataOject
s which uses the utility function printHead
.