| EList-class {limma} | R Documentation |
Simple list-based classes for storing expression values (E-values) for a set of one-channel microarrays.
EListRaw holds expression values on the raw scale.
EList holds expression values on the log scale, usually after background correction and normalization.
EListRaw objects are normally created by read.maimages.
In the future, EList objects are likely to be created normalizeBetweenArrays.
EList objects can be created by new("EList",E) where E is a list.
These classes contains no slots (other than .Data), but objects should contain a list component E as follows:
E: | numeric matrix containing the E-values (raw or log-2 expression ratios). Rows correspond to spots and columns to arrays. |
Optional components include:
weights: | numeric matrix of same dimensions as E containing relative spot quality weights. Elements should be non-negative. |
other: | list containing other matrices, all of the same dimensions as E. |
genes: | data.frame containing probe information. Should have one row for each probe. May have any number of columns. |
targets: | data.frame containing information on the target RNA samples. Rows correspond to arrays. May have any number of columns. |
Valid EList or EListRaw objects may contain other optional components, but all probe or array information should be contained in the above components.
These classes inherit directly from class list so any operation appropriate for lists will work on objects of this class.
In addition, EList objects can be subsetted and combined.
EList objects will return dimensions and hence functions such as dim, nrow and ncol are defined.
ELists also inherit a show method from the virtual class LargeDataObject, which means that ELists will print in a compact way.
Gordon Smyth
02.Classes gives an overview of all the classes defined by this package.
ExpressionSet-class is a more formal class in the Biobase package.