[BioC] annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)

[Marc Carlson]

Hi Hari,

To get the data that you need from Agilent you need to register with 
their earray site here:

https://earray.chem.agilent.com/earray/

And then once you can log in, you should be able to find files with the 
information you need.  The Agilent site can be surprisingly difficult to 
use, but the data is usually in there.

Then once you have the data you will want to look at this vignette:

http://www.bioconductor.org/packages/2.10/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf



   Marc




On 08/07/2012 10:45 AM, Hari Easwaran wrote:
> Thanks Jim. I saw a paper using hgug4110b.db, hence wanted to clarify.
> I could not find the annotation file in the Agilent website.
>
> Anyways, thanks for your help.
>
> Hari
>
> On Tue, Aug 7, 2012 at 1:27 PM, James W. MacDonald<jmacdon at uw.edu>  wrote:
>
>> Hi Hari,
>>
>>
>> On 8/7/2012 12:30 PM, Hari Easwaran wrote:
>>
>>> Dear all,
>>> Is the annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)
>>> array available in Bioconductor. I am not sure if "hgug4110b.db" is the
>>> one
>>> I am looking for.
>>>
>> I am pretty sure that is not what you want. Agilent had microarrays called
>> the G4110A and G4110B, and those are what the hgug4110a.db and hgug4110b.db
>> are designed for.
>>
>> I am not familiar with Agilent's website, and a cursory glance didn't
>> result in me finding the annotation file for this array. But if you have
>> such a thing (with say columns that contain the Agilent ID and another with
>> Gene, UniGene, RefSeq, etc type IDs), then you can create your own pretty
>> easily using the AnnotationDbi package.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>
>>   Can someone help?
>>> Thanks is advance.
>>>
>>> Hari
>>>
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>>>
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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
>>
>>
> 	[[alternative HTML version deleted]]
>
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