KMC on Affy dChip data

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Tamra
2009-06-18
2013-05-20
  • Tamra

    Tamra - 2009-06-18

    Hello,
    I have some experience working with meV for 2 color arrays, and really like the analysis options.  We recently did some Affymetrix arrays with an academic collaborator.  Our collaborator helped us to do initial processing (normalization, filtering, compare samples, etc.) of our Affy arrays using dChip.  Now we would like to do K-means clustering on our Affy dChip data.  (I am also interested in performing SAM.)  I would like very much to use meV for this.  I understand I can load TDMS files into MeV, but not sure which dChip output files are best to use ("compare samples"?),and how to format for MeV processing.  I appreciate any advice.  Thanks for your support.
    Tamra

     
    • Sarita Nair

      Sarita Nair - 2009-06-19

      Hi Tamra,

      My colleague here mentioned that dChip does let you export the normalized files as tab delimited text. Once you have it in a tab delimited format, you should be able to use the TDMS file loader to load your data.

      Thanks,
      Sarita

       
    • Tamra

      Tamra - 2009-06-19

      Yes, thank you.  I understood I can load the dChip files.  My question is WHICH dChip output files should be used for K-means clustering.  I'm not sure what data values MeV uses for KMC.
      Tamra

       
      • Sarita Nair

        Sarita Nair - 2009-06-19

        I am not sure what you mean by "What data values MeV uses for KMC".
        MeV uses the normalized data  that you loaded.

        Here is the URL for dChip help:
        http://www.hsph.harvard.edu/~cli/complab/dchip/model-based%20expression.htm

        Scroll down to the Export expression values section. This should give you pointers on HOW TO EXPORT YOUR NORMALIZED DATA AS A TAB DELIMITED TEXT file. Once you do that, you can use the TDMS loader in MeV to load your data.

        Sarita

         

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