R help - Feb 2005 - Conversion of Affy IDs , LocusLink IDs etc...

Hi,

I was trying to compare differential expression data
from multiple studies ( 4 dataset downloaded from NCBI
GEO). The expression dataset are from Affy, as well as
cDNA (dual channel) platforms. Before I conduct
analysis, I have to map the gene IDs so that the
different genes are comparable.

Which packages, and what commands do I need for this?

thanks,

Pankaj

Pankaj Chopra wrote:
> Hi,
> 
> I was trying to compare differential expression data
> from multiple studies ( 4 dataset downloaded from NCBI
> GEO). The expression dataset are from Affy, as well as
> cDNA (dual channel) platforms. Before I conduct
> analysis, I have to map the gene IDs so that the
> different genes are comparable.
> 
> Which packages, and what commands do I need for this?

Take a look at the Bioconductor project:
http://www.bioconductor.org/

Uwe Ligges
> thanks,
> 
> Pankaj
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

You may also be interested in the following, which point out potentially
severe problems with such metanalyses. 

http://www.cbs.dtu.dk/courses/norfa2004/Extras/5_1_Yves_TiG_meta-analysis_Ar
ticle.pdf

http://www.clinchem.org/cgi/content/full/47/8/1350

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box
 
 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Uwe Ligges
> Sent: Thursday, February 10, 2005 10:29 AM
> To: Pankaj Chopra
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] Conversion of Affy IDs , LocusLink IDs etc...
> 
> Pankaj Chopra wrote:
> 
> > Hi,
> > 
> > I was trying to compare differential expression data
> > from multiple studies ( 4 dataset downloaded from NCBI
> > GEO). The expression dataset are from Affy, as well as
> > cDNA (dual channel) platforms. Before I conduct
> > analysis, I have to map the gene IDs so that the
> > different genes are comparable.
> > 
> > Which packages, and what commands do I need for this?
> 
> 
> Take a look at the Bioconductor project:
> http://www.bioconductor.org/
> 
> Uwe Ligges
> 
> > thanks,
> > 
> > Pankaj
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>