[BioC] CDF issue

[Mathe, Ewy (NIH/NCI) [F]]

Hello everyone,

Switching to the oligo package did the trick!

Many thanks,
Ewy

-----Original Message-----
From: Mathe, Ewy (NIH/NCI) [F] 
Sent: Thursday, November 06, 2008 7:50 AM
To: Mark Robinson; laurent
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] CDF issue

Mark, Laurent, and Benilton,

Thank you all for your comments, I will give your suggestions a try and
let you know.

Best,
Ewy


-----Original Message-----
From: Mark Robinson [mailto:mrobinson at wehi.EDU.AU]
Sent: Thu 11/6/2008 7:07 AM
To: laurent
Cc: Mathe, Ewy (NIH/NCI) [F]; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] CDF issue
 
Hi Ewy.

Just to follow up on Laurent's post.  I'm afraid I can't speak to the  
problems you are having below ... but I do know of at least 3 ways to  
preprocess Gene 1.0 ST data (say, with RMA) in R:

1. aroma.affymetrix
http://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1
(can follow mostly the same steps as in
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-ana
lysis)

2. xps package
https://stat.ethz.ch/pipermail/bioconductor/2008-May/022267.html

3. as you were doing, perhaps spelled out a little better at (+ using  
'rma' in the oligo package):
http://article.gmane.org/gmane.science.biology.informatics.conductor/189
63/

HTH,
Mark



On 06/11/2008, at 5:24 PM, laurent wrote:

> 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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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852