getExpressionSet {Risa} | R Documentation |
Retrieves an ExpressionSet for a DNA microarray assay.
getExpressionSet(isa, assay.filename)
isa |
An object from the |
assay.filename |
A character vector with the assay filename of the microarray assay. |
It returns an ExpressionSet
.
Alejandra Gonzalez-Beltran
affy
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]])