[BioC] CDF issue

[laurent]

Hi Mathe,

For historical reasons, the "annotation" is the association between
probe sets and gene name, chromosomal location, etc...
The CDF data structure models the files with extension .cdf (Chip
Definition File), and contains the association between probe position
on the array and the probe set the probe belongs to.

This earlier post is related to the problem you are having:
https://stat.ethz.ch/pipermail/bioconductor/2007-November/020188.html



L.

On Wed, 2008-11-05 at 18:21 -0500, Mathe, Ewy (NIH/NCI) [F] wrote:
> Hello,
> 
>  
> 
> My goal is to preprocess and normalize Affy Mouse Gene 1.0 ST arrays but am having difficulty doing so in R.
> 
>  
> 
> I have successfully built my own annotation package, which has the name "pd.mogene.1.0.st.v1".  However, after loading the package and reading in my CEL files, it does not automatically annotate the dataset and outputs the following:
> 
>  
> 
> > data
> AffyBatch object
> size of arrays=1050x1050 features (14 kb)
> cdf=pd.mogene.1.0.st.v1 (??? affyids)
> number of samples=8
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain pd.mogene.1.0.st.v1
> Library - package pd.mogene.1.0.st.v1cdf not installed
> Data for package affy did not contain pd.mogene.1.0.st.v1cdf
> Bioconductor - could not connect
> In addition: Warning messages:
> 1: In readLines(biocURL) :
>  cannot open: HTTP status was '503 Service Unavailable'
> 2: missing cdf environment! in show(AffyBatch)
> 3: In readLines(biocURL) :
>  cannot open: HTTP status was '503 Service Unavailable'
> 
>  
> 
> 
> 
> For some reason, the package names are not synchronized but I cannot figure out how to rebuild the package by specifying the name.  This is the code I used to build the package:
> 
>  
> 
> pgfFile <- "MoGene-1_0-st-v1.r3.pgf"
> 
> clfFile <- "MoGene-1_0-st-v1.r3.clf"
> 
> transFile <- "MoGene-1_0-st-v1.na26.mm9.transcript.csv"
> 
> probeFile <- "MoGene-1_0-st-v1.probe.tab"
> 
> pkg <- new("AffyGenePDInfoPkgSeed", author = "em", email =
> 
> "mathee at mail.nih.gov", version = "0.0.1", genomebuild = "thegenomebuilddate",
> 
> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
> 
> transFile = transFile, probeFile = probeFile)
> 
> makePdInfoPackage(pkg,destDir=".")
> 
>  
> 
> Thanks in advance for any input you can give me on this!
> 
>  
> 
> Ewy
> 
>  
> 
> Ewy Math, Ph. D.
> 
> Laboratory of Human Carcinogenesis
> 
> National Cancer Institute, NIH
> 
> 37 Convent Drive
> 
> Building 37, Room 3068
> 
> Bethesda, MD  20892-4255
> 
> Tel: 301-496-5835
> 
> Fax: 301-496-0497
> 
>  
> 
> 
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> 
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