Analysis of duplicate spots and dye swap expt

  • Prasanta Subudhi

    I need some help in analysis of my microarray data using TM4 package. I hope some body can come forward to help.

    1. Since the text files are from agilent , I used the express converter to convert to MeV files successfully.  In the converted files, each was given an unique ID. But the probes are duplicated i.e. 22000 genes but total spots are 44000. Is there any way to get average intensity level for each of the 22000 probes using MeV?

    2.Again two slides were labeled in a conventional way and the other two Cy3: Cy5 label was reversed. How to analyze all four arrays in MeV ?

    Thanks in advance for your help.


    • John Braisted

      John Braisted - 2009-06-24

      Hi PK,

      I work right across from Wei Liang, the person that developed Midas, TM4's normalization and filtering tool.  Midas has the capability to take geometric means of replicate spots on a slide and provide a single mean for each replicate set.  The feature is called In-slide replicates analysis and it will enter the mean in the first row of the replicate set.  Other rows in the file (further down) are set to 0 and 0 for IA and IB.  These empty rows can later be filtered in MeV using 'Adjust Data->Data Filters->Percentage Cutoff Filter'.

      Midas will work on your .mev files. 

      Midas web page:

      Here's the help email for midas,  You probably want to contact Wei when running this for some advice.  The files will require a column appended that indicates which spots are replicates.  Wei will be happy to assist with additional information on this feature of Midas.

      John Braisted


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