[BioC] CDF for Mouse gene 1.0 ST

[Michal Okoniewski]

Hi Henrik, Marco & all

The issue with CDF files for exon arrays it is not that obvious. 
They are really "unsupported" and it means that they include "probesets"
of background probes in the form of loooong ones and single-probe - so
they 
cannot be used in BioConductor. I have done some manual editing of the
CDFs
removing background and controls (http://xmap.picr.man.ac.uk/cdf) 
so they may be used with RMA and plier. 

Having a quick look into the "unsupported CDF" for Mouse Gene 1.0ST
array, 
I see the same problem - control/background probes groupped in huge
"probesets"
that make the CDF useless for summarization without painstaking
preprocessing/cleaning.
But the program that I used to clean exon CDFs does not work for gene
CDFS :|

So Marco - when you find the way around the Mouse Gene CDF  - let us
know..

Cheers & saluti, 
Michal  

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik
Bengtsson
Sent: 17 November 2007 16:34
To: Marco Fabbri
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] CDF for Mouse gene 1.0 ST

Hi,

you will in (almost?) all case find links to annotation files, sample
data etc for Affymetrix arrays at the corresponding "Support Materials"
page.  For chip types where Affymetrix support CDF files you'll find the
CDF files within a large zipped "Library File".  For exon arrays,
Affymetrix do not support CDF files, but will often still provide one
separately (often in an ASCII format), as is also the case for the Mouse
Gene 1.0 ST array.

Have a look at

 
http://www.affymetrix.com/support/technical/byproduct.affx?product=mogen
e-1_0-st-v1

and you'll see there is a CDF file.

FYI, you can convert a CDF in an ASCII format into a binary format using
convertCdf() in affxparser ***and that is highly recommended*** (for
speed and memory reasons).

/Henrik

On Nov 17, 2007 5:47 AM, Marco Fabbri <fabbri.marco at gmail.com> wrote:
>  I was looking for a cdf file
>
> Marco
>
>
>  Hi
> Marco,
> Are these not what you want?
>
>    from here:
>
[1]http://www.affymetrix.com/support/technical/byproduct.affx?product=mo
gene
>    -1_0-st-v1
>    []  [2] MoGene-1_0-st-v1 Annotations CSV README (26 KB, 9/5/07)
>    []   [3]  MoGene-1_0-st-v1 Transcript Cluster Annotations, CSV (11
MB,
>    9/17/07)
>    Pingzhao
>
>
> --
> ---------------------------------------
> Marco Fabbri
> Istituto Clinico Humanitas
> via Manzoni, 56
> 20089 Rozzano (Mi)
> Tel. 028224 5130
> Fax 028224 5101
>
> _______________________________________________
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>

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