[BioC] GEO annotations

[Marc Carlson]

Hi Assa,

I am afraid that in order to help you we would need to know more
specifics about what you are trying to do.  You might want to read the
posting guide here:

http://www.bioconductor.org/docs/postingGuide.html

Also, since it seems that you might be simply trying to match a probe to
a gene, if that is what youy are trying to do we can probably help with
that.  There are vignettes in the AnnotationDbi package that can
probably get you started (assuming that you know what platform that
probe originated from):

http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html


  Marc




On 05/11/2010 08:16 AM, Sean Davis wrote:
> On Tue, May 11, 2010 at 11:01 AM, Assa Yeroslaviz <frymor at gmail.com> wrote:
>
>   
>> well not exactly,
>>
>> I found first the soft file on the server before I found out what GSE File
>> I
>> need. :~)
>> I found the GEOquery only later.
>>
>> What I didn't get there was how do i find what GSE i needed. Just by
>> stating
>> the A-52... Number didn't get me anywhere. I have had to look on the server
>> which chip ahs these annotations ( i didn't even know if this is an Agilent
>> or an affymetrix chip)
>>
>> Is there a way of making such a query using GEOquery?
>> If i understood it correctly, GEOquery is only to get GEO-annotation from
>> the server but not the other way around.
>>
>> Am i wrong?
>>
>>     
> If you know the GPL you want, GEOquery can download it and put it into R
> data structures.  If you are starting from a GSE (are you?), GEOquery will
> download that AND the associated annotation automatically.
>
> If your use case is to start with a probe ID, that isn't something that GEO
> was designed to deal with, at least as a download.  With a single probe, you
> could, of course go here:
>
> http://www.ncbi.nlm.nih.gov/geo/
>
> Do a gene profile search and then from there you will have your GPL
> annotation.
>
> Perhaps I'm not clear on what you are trying to do, though.  If you want
> more input, could you clarify what you are trying to do (bigger picture)?
>
> Sean
>
>
>
>   
>> On Tue, May 11, 2010 at 16:53, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>>     
>>>
>>> On Tue, May 11, 2010 at 10:51 AM, Assa Yeroslaviz <frymor at gmail.com
>>> wrote:
>>>
>>>       
>>>> Hi Sean,
>>>>
>>>> Thankx for the answer, but I think I found a solution.
>>>> I have for example the GEO name A_52_P431770
>>>> it's from the mouse genome (GSE14293) and I wanted to have the gene
>>>> symbols.
>>>> But I downloaded the complete GSE file and will merge it with my gene
>>>> list.
>>>>
>>>> If there are any other simpler /more efficient ideas, I would like to
>>>>         
>> hear
>>     
>>>> about them.
>>>>
>>>>
>>>>         
>>> You are using GEOquery, correct?  (hint, hint....)
>>>
>>> Sean
>>>
>>>
>>>       
>>>> On Tue, May 11, 2010 at 16:47, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>>
>>>>         
>>>>>
>>>>> On Tue, May 11, 2010 at 10:08 AM, Assa Yeroslaviz <frymor at gmail.com
>>>>> wrote:
>>>>>
>>>>>           
>>>>>> Hello  everybody,
>>>>>>
>>>>>> Is there a way of converting GEO annotations to gene names?
>>>>>> I have a list of GEO annotattions, but I would like to work with the
>>>>>> "real"
>>>>>> gene names.
>>>>>> I was wondering whether there is a way of coverting a list of GEO
>>>>>> annotation
>>>>>> to its official (HUGO, NCBI, etc..) names and/or vice versa.
>>>>>>
>>>>>>
>>>>>>             
>>>>> Hi, Assa.  You'll probably need to provide a concrete example.  "GEO
>>>>> annotation" is not, unfortunately, a well-defined concept.
>>>>>
>>>>> Sean
>>>>>
>>>>>
>>>>>           
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>
>>>       
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