[BioC] Using annotation package how can I convert the probe > ID's to Gene names.

[Paul Geeleher]

Whoops yes I see that now, I guess you first need to figure out what
kind of gene ids you have. That DAVID tool I spoke of can often
autodetect the type of gene id you are trying to convert if they are
in its database.

Paul.

On Wed, Jan 12, 2011 at 11:06 AM, Budhayash Gautam
<budhayashgautam at gmail.com> wrote:
> Thanks Paul for reply,
>
>  no these are not affy ids , i am working on two color data.
>
> On Wed, Jan 12, 2011 at 4:30 PM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
>> Are they affy ids? Maybe the gene ID conversion tool might be able to
>> help: http://david.abcc.ncifcrf.gov/conversion.jsp
>>
>> Paul.
>>
>> On Wed, Jan 12, 2011 at 9:42 AM, Budhayash Gautam
>> <budhayashgautam at gmail.com> wrote:
>>> Hello friends,
>>>
>>> i am working on some SMD two color data for Toxoplasma gondii , i have
>>> done differential expression analysis. Now i want to annotate these
>>> genes,
>>>
>>> now the problem is that how can i convert the probe ID's to Gene names
>>> using annotation package and with what database because there is no
>>> database in bioconductor related to t. gondii.
>>>
>>> if i have to pick these gene names from NCBI then how can i link or
>>> retrieve this information from ncbi collectively as i have to do these
>>> annotation on the level of genome so no. of genes are in thousands...
>>>
>>> or if any one can suggest any reading material it will be helpful to
>>> me becoz i am stuck right now how to go ahead.....
>>>
>>> --
>>> BUDHAYASH GAUTAM
>>> Assistant Professor
>>> Department Of Computational Biology And Bioinformatics,
>>> Jacob School of Biotechnology & Bioengineering (JSBB)
>>> Sam Higginbottom Institute of Agriculture, Technology and Sciences
>>> (SHIATS)- Deemed University, Naini, Allahabad.
>>> U.P. 211007
>>>
>>> _______________________________________________
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>>>
>>
>>
>>
>> --
>> Paul Geeleher (PhD Student)
>> School of Mathematics, Statistics and Applied Mathematics
>> National University of Ireland
>> Galway
>> Ireland
>> --
>> www.bioinformaticstutorials.com
>>
>
>
>
> --
> BUDHAYASH GAUTAM
> Assistant Professor
> Department Of Computational Biology And Bioinformatics,
> Jacob School of Biotechnology & Bioengineering (JSBB)
> Sam Higginbottom Institute of Agriculture, Technology and Sciences
> (SHIATS)- Deemed University, Naini, Allahabad.
> U.P. 211007
>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com