mev-tm4-users

[Mev-tm4-users] What are the procedure to identify differentially expressed genes?

[Peng Yu <pen...@gm...>]

Hi,

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


Regards,
Peng

Re: [Mev-tm4-users] What are the procedure to identify differentially expressed genes?

[Eleanor H. <ele...@ji...>]

Hi Peng,

We don't do much with this mailing list anymore, so I took the liberty 
of posting your question on the SourceForge help forums for MeV at 
https://sourceforge.net/forum/message.php?msg_id=7529963 . I also posted 
what I hope is a useful answer.

Eleanor


Peng Yu wrote:
> Hi,
>
> 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
>
>
> Regards,
> Peng
>
> ------------------------------------------------------------------------------
> _______________________________________________
> mev-tm4-users mailing list
> mev...@li...
> https://lists.sourceforge.net/lists/listinfo/mev-tm4-users
>