| coerce {convert} | R Documentation |
Convert between limma, marray and Biobase data objects.
Objects can be converted (coerced) from one class to another using
as(object, Class) where object is an object to convert
and Class is the name of the class to convert to. The following
conversions are provided:
| From: | To: |
RGList | marrayRaw |
marrayRaw | RGList |
MAList | marrayNorm |
marrayNorm | MAList |
RGList | exprSet |
MAList | exprSet |
marrayRaw | exprSet |
marrayNorm | exprSet |
Note that RGList and marrayRaw objects are coerced to
exprSet in such a way that green and red channel intensities are stored in alternate
columns of the exprs slot expression matrix. This means that the resulting
exprSet object has twice as many columns as the original object.
On the other hand, MAList and marrayNorm are coerced so
that the resulting exprs slot contains log-ratios (M-values)
and the exprSet object has the same number of columns as the
original object.
In this case, information on the A-values is lost.
Gordon Smyth
as in the methods package.
x <- new("RGList")
y <- as(x,"marrayRaw")
x <- new("marrayRaw")
x@maGf <- matrix(rnorm(5*2),5,2)
x@maRf <- matrix(rnorm(5*2),5,2)
y <- as(x,"RGList")
y <- as(x,"exprSet")
x <- new("MAList")
y <- as(x,"marrayNorm")
x <- new("marrayNorm")
x@maM <- matrix(rnorm(5*2),5,2)
x@maA <- matrix(rnorm(5*2),5,2)
y <- as(x,"MAList")
y <- as(x,"exprSet")
x <- new("MAList")
x$M <- matrix(rnorm(5*2),5,2)
y <- as(x,"exprSet")