[BioC] equivalent probes between microarray platforms

[Robert Gentleman]

On Fri, Oct 15, 2004 at 06:06:39PM +0200, Benjamin Haibe-Kains wrote:
> Hi all,
> 
> I would want to compare results from different article using different 
> micrarray platforms:
> 
>     1. I have experiments hybridized on the Affymetrix hgu133plus2 and i 
> want to compare them against those from affymetrix hu6800 chip.  In the 
> Affymetrix website, I have not found the probes equivalent on the two 
> platforms in the array comparison spreadsheets. I have the unigene 
> cluster id and the genbank accession number for these probes ... How can 
> I safely find the equivalent probes ?


  matchprobes, has for some number of years now ,provided this
  functionality. 

> 
>     2. I have the same problem to resolve but from the Affy hgu133plus2 
> chip and a specific cDNA platform. Again I have trhe unigene cluster id 
> and the genbank accession number.
> 
  there are many issues here, you can do some sequence matching. You
  might alow want to look at, since just matching probes is not always
  the best thing to do.

  title =        {A cross-study comparison of gene expression studies
                  for the molecular classification of lung cancer},
  author =       {Parmigiani, G. and Garrett-Mayer, E. and Anbazhagan,
                  R. and Gabrielson, E.},
  journal =      {Clincal Cancer Research},
  year =         {2004},
  volume =       {10},
  pages =        {2922--2927}
}


  title =        {Combining multiple microarray studies and modeling
                  interstudy variation},
  author =       {Choi, J. K. and Yu, U. and Kim, S. and Yoo, O. J.},
  journal =      {Bioinformatics},
  year =         {2003},
  volume =       {19, Suppl. 1},
  pages =        {i84--i90},
}



> Can you help me ?
> 
> Thanks in advance :)
> 
> -- 
> Benjamin Haibe-Kains
> 	[http://www.ulb.ac.be/di/map/bhaibeka/]
> 
> 
> PhD student in the Machine Learning Group (MLG)
> 	[http://www.ulb.ac.be/di/mlg/]
> Universite Libre de Bruxelles (ULB)
> E-mail: bhaibeka at ulb.ac.be 
> 
> MicroArray Unity 
> 	[http://www.bordet.be/servmed/array/index.htm]
> Institut Jules Bordet (IJB)
> E-mail: benjamin.haibekains at bordet.be
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
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