[BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms

Kaj Chokeshaiusaha kajkajkajkajkaj at gmail.com
Sat Feb 16 16:20:59 CET 2013


Dear All,

I hope this won't be too tedious for you, please be patient with me.

I have found the bovine gene list from Agilent (
http://www.chem.agilent.com/cag/bsp/gene_lists.asp).

Is this what I need for making db package?

Best Regards,
Kaj

On Fri, Feb 15, 2013 at 7:54 PM, Kaj Chokeshaiusaha <
kajkajkajkajkaj at gmail.com> wrote:

> 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 at trm.uni-leipzig.de> 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 at uw.edu>
>>
>> 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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