Kaj Chokeshaiusaha | 15 Feb 13:54 2013
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Re: Have troubles with finding Annotations for Bovine and Rhesus\' platforms

Dear All,

I have loaded AnnotationForge. I will try my best to understand it. I will
certainly come up with more questions. Thank you very much for your helps.

Best Regards,
Kaj

On Fri, Feb 15, 2013 at 4:54 PM, Andreas Heider
<aheider@...>wrote:

> 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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