Andreas Heider | 15 Feb 10:54 2013
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Re: Have troubles with finding Annotations for Bovine and Rhesus\' platforms

Dear Kaj,
Jim was mostly correct. You will have to setup a annotation package for
your bovine chip, but don't worry, you can use Affymetrix' annotation files
to get it done using AnnotationForge. For your Rhesus chip you could try to
use the org.Mmu.eg.db or rhesus.db0 packages, but will need to convert your
probesets into some gene/transcript identifier first using Affymetrix'
annotations. Your mouse data can be used directly using one of the
mogene10* annotation packages, as Jim already pointed out.

Your approach involves some work, but is definitely possible.

Cheers,
Andreas

2013/2/14 James W. MacDonald <jmacdon@...>

> Hi Kaj,
>
>
> On 2/14/2013 11:48 AM, Kaj Chokeshaiusaha [guest] wrote:
>
>> Dear whom it may concern,
>>
>> I'm working with the platforms as following:
>> 1. Agilent-015354 Bovine Oligo Microarray (4x44K)
>>
>
> I don't think there is a .db package for this one. You could go to earray (
> https://earray.chem.agilent.**com/earray/<https://earray.chem.agilent.com/earray/>)
> and find the correct GeneList, and then use AnnotationForge to create one.
> It could be fun, and help you break out of that 'pure biologist' rut you
> appear to be in ;-D
>
>
>  2. Affymetrix GeneChip Rhesus Macaque Genome Array [Rhesus]
>>
>
> biocLite("rhesus.db")
>
>
>  3. Affymetrix GeneChip Mouse Gene 1.0 ST Array
>>
>
> biocLite("**mogene10sttranscriptcluster.**db")
>
> assuming that you have summarized at the transcript level (and IMO you
> should).
>
> Best,
>
> Jim
>
>
>
>> Since I'm quite pure biologist, I do have no idea how to find appropriate
>> annotations (.db) for these platforms. I need to use them for virtaulArray.
>>
>> Would you please help me?
>>
>> Best Regards,
>> Kaj
>>
>>   -- output of sessionInfo():
>>
>> sessioninfo()
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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