[BioC] Finding Annotation of CEL file formats

[Marc Carlson]

Hi Gundala,

Once you know that these are hgu133plus2 chips, you could learn it from 
the correspondingly named "hgu133plus2.db" package that Jim named by 
typing:

hgu133plus2ORGANISM

Similarly you can get a host of other gene-centric information from this 
package.


  Marc



James W. MacDonald wrote:
> Hi Gundala,
>
> Gundala Viswanath wrote:
>> Dear all,
>>
>> Given any CEL file, such as these:
>>
>> http://bioinf.boku.ac.at/pub/Chaix2008/CEL/supplCELdata.zip
>>
>> With BioConductor Is there a way we can find:
>>
>> 1. Which organism they come from?
>
> The only information you can glean from the celfile will be particular 
> to the celfile itself. So you can determine that they are hgu133plus2 
> chips, but I don't think you can determine the organism.
>
> Of course you could just download the target description file and use 
> that:
>
> http://bioinf.boku.ac.at/pub/Chaix2008/target_info.txt
>
>> 2. Which organism's tissue they come from?
>
> Again, probably not.
>
>> 3. What are the probe names/gene name involved?
>
> The easiest way would be to use the hgu133plus2.db package.
>
> Best,
>
> Jim
>
>
>
>>
>> I looked at "affy" package but I can't seem to find
>> ways to get what I wanted above. But maybe I am wrong.
>>
>> - Gundala Viswanath
>> Jakarta - Indonesia
>>
>> PS: Original URL for the data is this
>> http://bioinf.boku.ac.at/pub/Chaix2008
>>
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>