Dear Bioconductor,
I would like to use the affylmGUI but not with a chip from
Bioconductor. The problem is, I have my own cdf-file and I want to use
this one instead of the provided by Affymetrix. How should I go on?
Many thanks in advance,
Best,
Paul C. Schr?der
--
--
Paul C. Schr?der
PhD Student
Department for Proteomics & Bioinformatics
Center for Applied Medicine (CIMA)
Avda. P?o XII, 55
31008 Pamplona
Tel. 948 194700
<pschrode at="" alumni.unav.es="">
----------------------------------------------------------------
Este mensaje ha sido enviado desde https://webmail.unav.es
Hi Paul,
Paul Christoph Schr?der wrote:
> Dear Bioconductor,
>
> I would like to use the affylmGUI but not with a chip from
> Bioconductor. The problem is, I have my own cdf-file and I want to
use
> this one instead of the provided by Affymetrix. How should I go on?
You will need to make a cdf package using the makecdfenv package.
There
is a vignette in makecdfenv that shows how to make a package, and then
you should consult the 'Writing R Extensions' manual that comes with
R,
which shows how to install the package.
Best,
Jim
>
> Many thanks in advance,
>
> Best,
> Paul C. Schr?der
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Hi Paul,
this feature has been asked for recently. The previous
maintainer/programmer has
gone some way down this path, but it is not functioning yet. I hope to
look at
this early in December. When it works I'll put it in the devel version
of
Bioconductor and let the list know,
cheers,
Keith
========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
========================
Paul Christoph Schr?der wrote:
> Dear Bioconductor,
>
> I would like to use the affylmGUI but not with a chip from
> Bioconductor. The problem is, I have my own cdf-file and I want to
use
> this one instead of the provided by Affymetrix. How should I go on?
>
> Many thanks in advance,
>
> Best,
> Paul C. Schr?der
I am not too familiar with the affylmGUI package but I assume it
builds on the structures from affy. In that case you should be able
to do it manually:
you make a cdf environment using "makecdfenv". You can either make
a package like Jim is saying, which is better in the long run (but
slightly more complicated especially on windows) or you can just have
a cdf environment in your workspace. Then you need to link your data
to this package. Presumably you have read in the data using affy, or
perhaps using a GUI. Anyway, the data should bve in the form of an
"AffyBatch" object. Say the data is called something like paulData.
Then you just do
R> paulData at cdfName <- "ENVNAME"
with ENVNAME the name of your cdfenv. A slightly more explicit script
would be something like
R> customCdf <- makecdfenv(...)
R> paulData <- ReadAffy(...)
R> paulData at cdfName <- "customCdf"
check by just doing a
R> paulData
If the cdfName has been set correctly and you have a cdf environment
in your global workspace, the printing should work without problems.
Kasper
On Nov 18, 2006, at 3:15 AM, Keith Satterley wrote:
> Hi Paul,
>
> this feature has been asked for recently. The previous maintainer/
> programmer has
> gone some way down this path, but it is not functioning yet. I hope
> to look at
> this early in December. When it works I'll put it in the devel
> version of
> Bioconductor and let the list know,
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
> ========================
> Paul Christoph Schr?der wrote:
>> Dear Bioconductor,
>>
>> I would like to use the affylmGUI but not with a chip from
>> Bioconductor. The problem is, I have my own cdf-file and I want to
>> use
>> this one instead of the provided by Affymetrix. How should I go on?
>>
>> Many thanks in advance,
>>
>> Best,
>> Paul C. Schr?der
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/
> gmane.science.biology.informatics.conductor
