Hey Lucia,

I just want to note, that if you want to stick to the Affymetrix Power 
Tools, you can use PGF, CLF and MPS files rather than a CDF. I am 
normalize my gene arrays this way. These files are officially supported 
by Affymetrix and available on their web site.

Pascal


On 12/02/2010 08:11 PM, Lucia Peixoto wrote:
> Hi,
> thanks for all the help, I used to Affy powertools to get 
> normalization quickly using RMA
> I tried mouse 1.0 CDF but affy didn't like it
> I will work on a new pipeline using oligo
>
> Any advice on how to do array quality metrics coming from oligo?
>
> thanks again for all the help
>
> Lucia
>
>
> On Thu, Dec 2, 2010 at 6:11 AM, Pascal Gellert 
> <pascal.gellert@mpi-bn.mpg.de <mailto:pascal.gellert@mpi-bn.mpg.de>> 
> wrote:
>
>     Hi Lucia,
>
>     as far as I know are the Mouse Gene 1.1 ST Array Plates identical
>     to Mouse Gene  1.0 ST Cartridge Arrays. Meaning that you could use
>     the 1.0 CDF file for the 1.1 Plate!? And these can be normalized
>     with oligo as Mark suggested.
>
>
>     Pascal
>
>
>
>
>
>     On 01/-10/-28163 08:59 PM, Lucia Peixoto wrote:
>
>         Hi All,
>
>         I just got all my data back from my experiment and I can't
>         find the cdf file
>         for the  Mouse Gene 1.1 ST Array anywhere
>         anyone knows how to get it or do I have to build it myself?
>         thanks for your help
>
>         Lucia
>
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>
>
>
>


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