Hi, thanks. I've attached a script illustrating how to allocate an empty Aroma Cell Sequence (*.acs) file and then import probe sequences from an Affymetrix probe tab file. Hopefully that show to do it.
If you build UGP, UFL, ACS or other files, please consider sharing it
here. As soon as we got the new site for documentation up, we can
include such files there.
Cheers,
Henrik
PS. You want to do require("AffyCompatible") || stop("Package not
loaded: AffyCompatible"), incase the package is not installed.
On Thu, Jul 9, 2009 at 6:10 PM, James F.
Reid<james.r...@ifom-ieo-campus.it> wrote:
>
> Dear all,
>
> following the recent question that Michael posted to the list regarding
> the location of a CDF file for a particular chiptype
> (Mapping10K_Xba131), I have come up with a small script that downloads
> any particular CDF file by using the Bioconductor package
> AffyCompatible. To get this to work you need to install it and have an
> account with NetAffx. Having this set-up, then the answer to Michaels'
> question would be downloadCDF("Mapping10K_Xba131").
>
> Now I am working for the rest of the annotation data files required for
> doing copy-number and gene expression analysis within aroma.affymetrix.
> Since the annotation files (.csv) can also be downloaded in this way I
> think I can work out a solution for the .ufl and .ugp files but I don't
> really know how to go about creating the .acs files. Any ideas?
>
> Thanks,
> James.
>
> ################################################################################
> ##begin script
> ##
> ## download CDF files via NetAffx using AffyCompatible
> downloadCDF <- function(chiptype, overwrite = FALSE, verbose = TRUE) {
>
> ## check for cdf file in current directory
> cdfFile <- paste(chiptype, ".cdf", sep = "")
> if (length(dir(path = ".", pattern = cdfFile, full.names = TRUE,
> ignore.case = TRUE)) > 0) {
> if (overwrite) cat("Overwriting local CDF file.\n")
> else stop("Found local CDF file with overwrite set to FALSE.\n")
> }
>
> ## look for netAffxUser and netAffxPass stored in '.Rprofile'
> if (!exists("netAffxUser") | !exists("netAffxPass")) {
> cat("To prevent having to type your NetAffx username",
> "and password\neach time insert them in your",
> ".Rprofile\n")
> netAffxUser <- readline(prompt = "NetAffx username: ")
> netAffxPass <- readline(prompt = "NetAffx password: ")
> }
>
> require("AffyCompatible") ## takes time ...
> if (verbose) cat("Connecting to NetAffx...\n")
> ## initialize NetAffxResource
> rsrc <- NetAffxResource(user = netAffxUser, password = netAffxPass)
>
> ## check chiptype is available
> if (!chiptype %in% names(rsrc))
> stop("Couldn't find annotation files for chiptype ",
> chiptype, ".\n")
>
> cat("Downloading CDF library file for", chiptype,
> "from NetAffx. \n")
> tempCdf <- readAnnotation(rsrc,
> annotation = rsrc[[chiptype,
> "CDF Library File"]],
> content = FALSE)
> ## implicit assumption that all CDF files are zipped ...
> tempCdfName <- sub(".zip", "", tempCdf)
> zip.file.extract(tempCdfName, basename(tempCdf))
>
> file.copy(tempCdfName, basename(tempCdfName), overwrite = overwrite)
> ## clean up (for possible future overwrite within same session)
> file.remove(tempCdf, tempCdfName)
> }
> ##
> ## end script
> ########################################################################
>
>
> >
>
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Cytogenetics_Array,ACS.R
Description: Binary data
