[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.
More information about the Bioconductor
mailing list