[BioC] inquiry for CDF file

[Mark Cowley]

Hi Hyeong-Min,
Essentially, making a cdf environment (which I have done) won't 100%  
work with the new ST generation of chips, because now, each probe can  
be a part of multiple probesets, whereas in the past, this was never  
the case.
see https://stat.ethz.ch/pipermail/bioconductor/2007-June/017740.html

If you are using OSX or a unix/linux system, then you may also want to  
look at apt-probeset-summarize from the Affymetrix Power Tools. I find  
it to be VERY fast (less than 2 mins for any reasonable size ~20 chip  
experiment). The equivalent on windows is the Affymetrix Expression  
Console.
You will need the library file that Jim mentioned (from Affymetrix),  
and then it's a simple case of

apt-probeset-summarize -a rma -p *pgf -c *clf -o ./normalised *CEL

cheers,
Mark

On 15/07/2008, at 5:18 AM, Henrik Bengtsson wrote:

> Hi,
>
> you can also take a look at the aroma.affymetrix.  It handles common
> preprocessing methods for basically all chip types with a CDF file.
> All you need is a CDF file and the CEL files.  Here I mean a *real*
> CDF file and not a compiled Bioconductor "CDF" package.  To install
> aroma.affymetrix, go to
>
>  http://groups.google.com/group/aroma-affymetrix
>
> Works with any OS and approx 1GB of RAM.   Note also the comment on
> http://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1
> that suggest that you convert the ASCII MoGene-1_0-st-v1.CDF from
> Affymetrix into a binary CDF - that's easy with convertCdf() in
> 'affxparser'.
>
> Cheers
>
> Henrik
>
> On Mon, Jul 14, 2008 at 11:33 AM, James W. MacDonald
> <jmacdon at med.umich.edu> wrote:
>> Hi Hyeong-Min,
>>
>> Lee, Hyeong-min wrote:
>>>
>>> Hello.
>>> I'm looking for "mogene10stv1cdf" I couldn't find it on the  
>>> metadata.html.
>>> Could you please tell me where I can get it? Thank you for your  
>>> time.
>>
>> Unfortunately, we don't as yet supply the cdf file for this chip  
>> type.
>>
>> There are a couple of ways you can analyze these data, but none  
>> involves the
>> canonical makecdfenv/affy pipeline.
>>
>> You can use the successor to makecdfenv/affy, which is the
>> pdInfoBuilder/oligo pipeline (more to follow on this), or the xps  
>> package.
>> Non-BioC software includes aroma.affymetrix and Expression Console
>> (Affymetrix's own software).
>>
>> To use oligo to do the analysis you will first need to create a  
>> pdInfo
>> package. This package replaces all of the cdf, probe and annotation  
>> packages
>> that you may be used to. In order to build this package you will  
>> need to
>> download the library files (the first one on this page:
>> http://www.affymetrix.com/support/technical/byproduct.affx?product=mogene-1_0-st-v1) 
>> ,
>> the probe file in tabular format, and the transcript cluster  
>> annotation csv
>> file (both of which are found at the above URL).
>>
>> You then have to create a 'AffyGenePDInfoPkgSeed' object which you  
>> can then
>> use to build the package. The help page for this doesn't really  
>> cover this
>> sort of thing, so here is an example of how you would do so:
>>
>> pgfFile <- "MoGene-1_0-st-v1.r3.pgf"
>> clfFile <- "MoGene-1_0-st-v1.r3.clf"
>> transFile <- "MoGene-1_0-st-v1.na24.mm8.transcript.csv"
>> probeFile <- "MoGene-1_0-st-v1.probe.tab"
>>
>> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email =
>> "e at mail.net", version = "0.0.1", genomebuild = "thegenomebuilddate",
>> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
>> transFile = transFile, probeFile = probeFile)
>>
>> makePdInfoPackage(pkg)
>>
>> At this point you need to install the package. In any case, this is  
>> done at
>> a terminal prompt (or DOS prompt on Windows) using
>>
>> R CMD INSTALL thepackage
>>
>> You may also need to point to your library directory as well, using
>> something like
>>
>> R CMD INSTALL -l /path/to/lib thepackage
>>
>> If you are on linux, this Will Just Work (tm). However, if you are on
>> Windows or MacOS, you will need to get set up to build packages.  
>> Luckily
>> this isn't nearly as involved as in the past. See the R  
>> Installation and
>> Administration manual
>>
>> http://cran.r-project.org/doc/manuals/R-admin.html
>>
>> for your particular OS.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>> Best
>>> Hyeong-Min Lee
>>> Ph.D. candidate
>>> Program in Neurobiology
>>> Dept. Biomedical Sciences
>>> College of Medicine, FSU
>>> Lab; 850-645-2922
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
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>
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