[BioC] how to list the shared/common genes from between different genechips

[Robert Gentleman]

Hi Han,
  It depends on what level of sharing you want. You can do it at the 
level of UniGene/GenBank, 25mer, EntrezGene (and probably a few others).
That is probably the most important decision. One way to do this is to 
first decide what you want to match on and then  map all the probes on 
the chip to the identifier you are going to use (the annotation packages 
can be used for this and I suspect that biomaRt could do it as well)- 
and then use something like intersect to find the common ones.

  Best wishes
   Robert


weinong han wrote:
> Hi ,all
>  
> I  want to  list the shared/common genes from between different genechips, such as Affymetrix HG_U95A, Affymetrix HG_U95Av2, Affymetrix HG_U133A and some in-house genechips  with R2.1.0 patched under Windows XP. 
>  
> However, I didn't know what method/package is fit for the analysis. Anyone have the experience on it? Any suggestions and advice will be much appreciated.
>  
> Many thanks in advance.
>  
> 
> 
> Best Regards
>  
> Han Weinong  
> hanweinong at yahoo.com
> 
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