getExpressionSet {Risa} | R Documentation

## Retrieves an ExpressionSet for a DNA microarray assay.

### Description

Retrieves an ExpressionSet for a DNA microarray assay.

### Usage

    getExpressionSet(isa, assay.filename)

### Arguments

`isa` | An object from the `ISATab-class`.
`assay.filename` | A character vector with the assay filename of the microarray assay.

### Value

It returns an `ExpressionSet`.

### Author(s)

Alejandra Gonzalez-Beltran

### References

`affy`

### See Also

`ISATab-class`

### Examples

    data.dir <- system.file("extdata", package="Risa")
    isazip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa")
    path <- file.path(data.dir,"ARMSTRONG_ISA")
    isa <- readISAtab(zipfile = isazip, path = path, verbose =TRUE)
    path <- file.path(data.dir,"ARMSTRONG_ISA/")

    cel.files <- c("GSM510377_SA2006121413.CEL", "GSM510378_SA2006121414.CEL", "GSM510379_SA2006121415.CEL", "GSM510380_SA2006121416.CEL",
                    "GSM510381_SA2006121417.CEL", "GSM510382_SA2006121418.CEL","GSM510383_SA2006121419.CEL","GSM510384_SA2006121420.CEL",
                    "GSM510385_SA2006121421.CEL","GSM510386_SA2006121427.CEL", "GSM510387_SA2006121428.CEL", "GSM510388_SA2006121429.CEL",
                    "GSM510389_SA2006121440.CEL","GSM510390_SA2006121441.CEL", "GSM510391_SA2006121442.CEL")

    base.url <- "http://perdera.sph.harvard.edu/biidata/microarray/study_ARMSTRONG-S-3_3Zd4KeJNJ7/raw_data/"

    ###########download all the cel files - this is commented out, uncomment the following two lines if you want to build the expression set
    #lapply(cel.files, function(x) download.file(paste(base.url, x, sep=""), destfile=paste(path, x, sep="")))
    #getExpressionSet(isa, isa@assay.filenames[[1]])

[Package Risa version 1.29.0 Index]