| 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
exprSets 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")