Question: Problem with makePDpackage in makePlatformDesign and getCdfInfo in affy
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gravatar for Benjamin Lansdell
11.4 years ago by
Benjamin Lansdell30 wrote:
Dear list, I have been working with a custom drosophila tiling array for which I have a .bpmap file and some .cel files. I have created a package using the makePlatformDesign package via: > makePDpackage("./antisense_untrimmed.bpmap", manufacturer = "affymetrix", type = "tiling", extra = list(packagename = "pd.antisense.untrimmedcdf", package.path = ".", maintainer = "Ben Lansdell<lansdel at="" wehi.edu.au="">", author = "Ben Lansdell", version = "0.5-1", unlink = TRUE, verbose = TRUE)) which seems to work and install fine. Is this package then able to read in .cel files via ReadAffy() so I can try GCRMA background correct on the resulting AffyBatch or am I limited to using read.celfiles() in oligo to create a TilingFeatureSet object which doesn't have such functions. Trying ReadAffy I get: > celfiles = ReadAffy(filenames = list.celfiles()[1:3], cdfname = "pd.antisense.untrimmedcdf") > celfiles AffyBatch object size of arrays=2560x2560 features (13 kb) cdf=pd.antisense.untrimmedcdf (??? affyids) number of samples=3 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain pd.antisense.untrimmedcdf <s4 object="" of="" class="" "platformdesign"=""> Data for package affy did not contain pd.antisense.untrimmedcdf Bioconductor - pd.antisense.untrimmedcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) With: > traceback() 7: stop(paste("Could not obtain CDF environment, problems encountered:", paste(unlist(badOut), collapse = "\n"), sep = "\n")) 6: getCdfInfo(object) 5: featureNames(object) 4: featureNames(object) 3: cat("number of genes=", length(featureNames(object)), "\n", sep = "") 2: function (object) standardGeneric("show")(<s4 object="" of="" class="" "affybatch"="">) 1: function (object) standardGeneric("show")(<s4 object="" of="" class="" "affybatch"="">) Looking inside getCdfInfo() the problem seems to be when it calls cdfFromLibPath() so: > cdfFromLibPath("pd.antisense.untrimmedcdf") [1] "Checking to see if package pd.antisense.untrimmedcdf is already installed" [1] "The package pd.antisense.untrimmedcdf is already loaded" Class........: platformDesign Manufacturer.: Affymetrix Genome Build.: hg12 Error in geometry(object) : no slot of name "geometry" for this object of class "platformDesign" which is as far I've gotten. Is there a way around this or is what I'm trying not possible? Cheers, Ben
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