| array2ade4 {made4} | R Documentation |
Converts input data into a data.frame suitable for analysis
in ADE4. This function is called by bga and other made4
function.
array2ade4(dataset, pos = FALSE, trans = TRUE)
dataset |
A matrix, data.frame,
exprSet or marrayRaw.
If the input is gene expression data in a matrix or data.frame. The
rows and columns are expected to contain the variables (genes) and cases (array samples)
respectively.
|
pos |
Logical indicating whether to add an integer to dataset, to generate positive data.frame. Required for
dudi.coa or dudi.nsc |
trans |
Logical indicating whether dataset should be transposed. Both between
group analysis, and coinertia analysis expect that the cases (array samples)
are contained in the rows and that the variables (genes) are in the columns. Thus the data.frame must
be transposed prior to analysis |
bga and other functions in made4 call this function and it is
generally not necessary to call array2ade4 this directly.
array2ade4 calls getdata, and will accept a matrix, data.frame,
exprSet or marrayRaw format. It
will also transpose data or add a integer to generate a positive data matrix.
If the input data contains missing values (NA), these must first be removed or imputed (see the R libraries impute() or pamr()).
Returns a data.frame suitable for analysis by ade4 or made4 functions.
Aedin Culhane
library(affy)
data(geneData)
class(geneData)
dim(geneData)
dim(array2ade4(geneData))
class(array2ade4(geneData))
eset <- new("exprSet", exprs=geneData)
eset
class(eset)
class(array2ade4(eset))
dim(array2ade4(eset))