[BioC] how to match the identifiers in multiple microarray data setsHan,

For arrays that have annotation packages built for them (nearly all affy arrays and a growing number of other manufacturers), you can use the annotate package, combined with the annotation package itself to get various identifiers associated with the probes on the array, such as refseq and entrez gene ID.  

Alternatively, you could use the biomaRt package or matchprobes package if you are looking at affy arrays only.

However, this is only part of the story, as comparing two different probesets from different platforms for the same gene is probably not going to produce useful results without some further work to "normalize" the results (where normalize is not a well-defined process in general).  If that is your goal, I would suggest that this is an area that has not been fully explored and is an area of research.  

In any case, meta-analysis of microarray data does not lend itself to a canned approach, at least not yet.  Do you have a specific question that you are trying to answer with a specific set of experiments?

Sean

  ----- Original Message ----- 
  From: weinong han 
  To: bioconductor@stat.math.ethz.ch 
  Sent: Tuesday, November 15, 2005 8:51 PM
  Subject: [BioC] how to match the identifiers in multiple microarray data sets


  Hi, Everybody, 
    
  Matching of identifiers is an important component when meta analysis 
  are implemented in the  microarray data sets from different labs and 
  different technologies. 

  As to matching of identifiers, at least two methods are suggested: 

  1. cluster ID and gene names were assigned to all of the cDNA clones 
  and Affymetrix probes based on  UniGene; 

  2. using accession numbers provided by Affymetrix and other 
  manufacturers and mapped them to the current version of the UniGene database; 

  Some use RefSeq identifiers. Would you have the experiences of meta 
  analysis on microarray data sets? Any advice and suggestions will be much 
  appreciatedon how to match identifiers and how to choose the suitable 
  statistical methods in meta analysis . 

  What packages include complete procedures of meta analysis of 
  microarray data sets? 

  Thanks again. 



  Best Regards 
    
  Han Weinong  
  hanweinong@yahoo.com 

                  
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