[BioC] Problem with makePDpackage in makePlatformDesign and getCdfInfo in affy

Benjamin Lansdell lansdell at wehi.EDU.AU
Wed Jul 16 10:46:07 CEST 2008

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 =  
 > 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)


 > 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  
[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?


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