[BioC] inquiry for CDF file

[Henrik Bengtsson]

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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