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 |
MAList | ExpressionSet |
marrayRaw | exprSet |
marrayNorm | ExpressionSet |
Note that RGList
and marrayRaw
objects are coerced to
exprSet
s 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
object has twice as many columns as the original object. There is intentionally no such conversion to the ExpressionSet
class, as it is intended for expression values, not intensities.
On the other hand, MAList
and marrayNorm
are coerced so
that the resulting exprs
slot contains log-ratios (M-values)
and the exprSet
or ExpressionSet
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.
##first set up some fake intensity matrices testRed = matrix(rnorm(5*2),5,2, dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2"))) testGreen = matrix(rnorm(5*2),5,2, dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2"))) ##some sample/target info testTarget = data.frame(slide=c("S1", "S2"), Cy3=c("T", "C"), Cy5=c("C", "T"), row.names=c("S1", "S2")) maT = new("marrayInfo", maLabels=c("S1", "S2"), maInfo= testTarget) ##now create instances and convert x <- new("RGList") x$R = testRed x$G = testGreen y <- as(x,"marrayRaw") x <- new("marrayRaw") x@maGf <- testGreen x@maRf <- testRed x@maTargets = maT y <- as(x,"RGList") y <- as(x,"exprSet") x <- new("MAList") y <- as(x,"marrayNorm") ##we construct a reasonably complete fake, small ##instance of the marrayNorm class x <- new("marrayNorm") x@maM <- testRed x@maA <- testGreen maTargets(x) = maT y <- as(x,"MAList") y <- as(x,"exprSet") x <- new("MAList") x$M <- testRed x$A <- testGreen x$targets = testTarget y <- as(x,"ExpressionSet")