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 components:
M: |
| numeric matrix containing the M-values (log-2 expression ratios). Rows correspond to spots and columns to arrays. |
weights: |
numeric matrix of same dimensions as M containing relative spot quality weights. Elements should be non-negative. |
other: |
list containing other matrices, all of the same dimensions as M. |
genes: |
| data.frame containing probe information. Should have one row for each spot. 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. Usually includes columns Cy3 and Cy5 specifying which RNA was hybridized to each array. |
MAList objects may contain other optional components, but all probe or array information should be contained in the above components.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.marrayNorm is the corresponding class in the marray package.