[BioC] gene universe

Barbara Cegielska barceg at ibch.poznan.pl
Mon Jul 6 15:04:27 CEST 2009


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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