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?
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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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
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