Genepix flagged

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cbala
2009-07-29
2013-05-20
  • cbala

    cbala - 2009-07-29

    I'm new at this and just getting my feet wet.

    I did my spot finding and manual flagging with GenePix. I've generated .mev and .ann files in expressconvert. How do I remove flagged features from analyses in Mev? More generally can manually remove features that I don't want to use in my analysis?

    thanks!

    Chris

     
    • John Braisted

      John Braisted - 2009-07-29

      Hi Chris,

      MeV doesn't read flags and have the capability to filter data based on flags or annotation.

      ExpressConverter converts gpr flags to the conventions used in .mev files.  The Midas normalization tool is responsible for reading flags and filtering data based on flags.  This typically happens before MeV. Midas can do this optional flag-based filtering during the data read.  If you don't want to perform any normalization (or if normalization has already been done), you could just read your data into Midas, select to use these filters, then write out the data.  There is an option in Midas to output the data that is trimmed into a separate file.

      The software, Ginkgo, that I mentioned in my direct email to you (sent earlier) has an annotation-based trim option.  In the current version of Ginkgo, this option is bundled in a module called CIP (Channel Intensity Processing).  The annotation-based filter can be run independently from other filters in this module.  Future Ginkgo releases will put this filter out on it's own but for now look for it under CIP.

      Wei Liang, the developer of Midas and Ginkgo, sits across from me and has helped with this response.  Wei supports both of these tools through midas@jcvi.org and ginkgo@jcvi.org.

      Thanks for your interest in MeV.

      John B.

       

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