Finding differentially expressed genes

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2009-07-27
2013-05-20
  • Eleanor Howe

    Eleanor Howe - 2009-07-27

    Question originally asked on the mev user help mailing list:

    I am new to MeV. Please bear with me if my question is primitive. I
    have the following normalized expression level file. ko* are for the
    knock out cases. wt* are for the control cases. I am wondering what
    the procedure I should follow to compute the list of differentially
    expressed genes. Can somebody help me?

    $ head output.txt
            koA-mth_HZ_5238_MST1_19389.cel  koB-mth_HZ_5238_MST1_19390.cel koC-mth_HZ_5238_MST1_19391.cel     koD-mth_HZ_5238_MST1_19392.cel    wt1-mth_HZ_5238_MST1_19385.cel     wt2-mth_HZ_5238_MST1_19386.cel    wt3-mth_HZ_5238_MST1_19387.cel  wt4-mth_HZ_5238_MST1_19388.cel
    10344615        7.07210987006919        7.01089258722033    7.2642627000072 6.92980486555595   7.72857978063884    6.91124431275741        7.45776182961327  7.21025349865986
    10344617        3.02519545040591        3.08697023169755    3.03203234085828  3.09846420636071 3.12487891156704    3.10727683101607        3.0544609560487 3.03353963677405
    10344619        3.20294677833793        3.20612630466463    3.17655303153672  3.13210443165341 3.1378507207366 3.21452663497659    3.31345050224224        3.09287042099817
    10344621        4.70984671316916        4.68863215464979    4.43705857330756  4.59970839525133 4.66911715996711    4.80422412543456        4.57334787499862  4.60736276830484
    10344623        7.79927399492793        7.78057650451938    7.72710416870418  7.68525205462879 7.66271776323834    7.65761154201622        7.67860029345257  7.80684426781102
    10344625        8.43869623252839        9.23986002214653    9.01482181726202  8.8450593076064  8.59194370149885    9.08344656110017        9.07468813004613  8.92291936928794
    10344626        10.0590964382247        9.75778614016683    9.66874458340189  9.91560261746937 9.97497585580347    9.90593250683953        9.72513220186519  10.0570156812405
    10344627        7.45353674141328        7.85528510695415    7.1239938834144 7.48673272391552   8.2401362665769 7.24092300626232    7.4348487408975 7.8999935331867
    10344628        10.1181530678991        10.2050144957479    10.0821326432175  10.2014962484731 10.3549307008668    9.97359523972773        9.82152593658235  10.0714458425003

     
    • Eleanor Howe

      Eleanor Howe - 2009-07-27

      There are several ways to find differentially expressed genes with MeV. Two of the most commonly used methods are the t-Test and SAM modules. A full explanation of how to use these two methods is found in the MeV manual.

      Eleanor

       

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