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")