[BioC] gene universe

[Robert Gentleman]

Hi Barbara,
   I don't think you are telling us enough (and also you are really
asking questions about how to do your analysis, which is not really
the purpose of the mailing list).  GOstats has a vignette and there is
a fairly extensive chapter in the case studies book
http://www.bioconductor.org/pub/biocases/
that describes how to use GOstats. topGO is another alternative and it
also has a good vignette - those should be on your reading list,

 best wishes
   Robert


On Mon, Jul 6, 2009 at 6:04 AM, Barbara Cegielska<barceg at ibch.poznan.pl> wrote:
> I have performed the gene selection and now what GOstats should do? As I
> know I should define  the gene universe. Is  it possible to use such code?
>
> b<-topTable(fit2,adjust="BH")
> GeneUniverse<-b$ID
>
> ##########################################################################################################
>> topTable(fit2,adjust="BH")
>  Block Row Column    ID    Name Status     logFC  AveExpr          t
>  P.Value    adj.P.Val        B
> 284     11   5      4  6280  S100A9 Oligos -3.005805 8.759735 -10.909033
> 5.670428e-08 5.800847e-05 8.673252
> 455     17   8      4  1495  CTNNA1 Oligos  2.094615 8.171560   7.826195
> 2.597774e-06 1.328761e-03 5.101945
> 841     35   3      1  6726    SRP9 Oligos  2.847275 7.485457   7.365179
> 5.031173e-06 1.562502e-03 4.464491
> 302     12   2      4  6279  S100A8 Oligos -2.650320 8.921910  -7.189676
> 6.516279e-06 1.562502e-03 4.213853
> 1015    37  26      4  5921   RASA1 Oligos  3.969762 7.122127   7.083314
> 7.636864e-06 1.562502e-03 4.059777
> 836     35   1      4 80762 NDFIP1x Oligos  2.231278 7.104562   6.693262
> 1.384104e-05 2.359898e-03 3.480477
> 1020    37  27      4  5582   PRKCG Oligos  1.760605 9.131416   6.580613
> 1.649671e-05 2.377431e-03 3.308953
> 927     37   8     10   840   CASP7 Oligos  2.263642 8.433187   6.504504
> 1.859183e-05 2.377431e-03 3.191988
> 854     35   7      4  4772  NFATC1 Oligos  2.453980 7.217102   6.035467
> 3.953147e-05 4.493411e-03 2.451879
> 794     33   5      4  6168  RPL37A Oligos  1.420032 7.933803   5.660002
> 7.392029e-05 7.562046e-03 1.835547
> ########################################################################################################
>
> Regards,
> B.
>
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>



-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org