Converts microarray input data into a data frame suitable for analysis in ADE4.

Description

Converts input data into a data.frame suitable for analysis in ADE4. This function is called by bga and other made4 function.

Usage

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array2ade4(dataset, pos = FALSE, trans = FALSE)

Arguments

dataset

A matrix, data.frame, ExpressionSet or marrayRaw-class. 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. Default is FALSE.

Details

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, ExpressionSet or marrayRaw-class 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()).

Value

Returns a data.frame suitable for analysis by ade4 or made4 functions.

Author(s)

Aedin Culhane

See Also

getdata,as in the Bioconductor package convert.

Examples

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library(affy)
data(geneData)
class(geneData)
dim(geneData)
dim(array2ade4(geneData))
class(array2ade4(geneData))

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