MAList-class {limma} | R Documentation |
A simple list-based class for storing M-values and A-values for a batch of spotted microarrays.
MAList
objects are usually created during normalization by the functions normalizeWithinArrays
or MA.RG
.
MAList
objects can be created by new("MAList",MA)
where MA
is a list.
This class contains no slots (other than .Data
), but objects should contain the following list components:
M : | numeric matrix containing the M-values or log-2 expression ratios. Rows correspond to spots and columns to arrays. |
A : | numeric matrix containing the A-values or average log-2 expression values |
weights : | numeric matric containing relative spot quality weights. Should be non-negative. |
printer : | list containing information on the process used to print the spots on the arrays. See PrintLayout. |
genes : | data.frame containing information on the genes spotted on the arrays. Should include a character column Name containing names for the genes or controls. |
targets : | data.frame containing information on the target RNA samples. Should include factor or character columns Cy3 and Cy5 specifying which RNA was hybridized to each array. |
All of the matrices should have the same dimensions.
The row dimension of targets
should match the column dimension of the matrices.
This class inherits directly from class list
so any operation appropriate for lists will work on objects of this class.
In addition, MAList
objects can be subsetted and combined.
RGList
objects will return dimensions and hence functions such as dim
, nrow
and ncol
are defined.
MALists
also inherit a show
method from the virtual class LargeDataObject
, which means that RGLists
will print in a compact way.
Other functions in LIMMA which operate on MAList
objects include
normalizeWithinArrays
,
normalizeBetweenArrays
,
normalizeForPrintorder
,
plotMA
and plotPrintTipLoess
.
Gordon Smyth
2.Classes gives an overview of all the classes defined by this package.
marrayNorm-class
is the corresponding class in the marrayClasses package.