gene universe

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Barbara Cegielska ▴ 200

@barbara-cegielska-3434

Last seen 9.6 years ago

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.

GOstats GOstats • 1.1k views

ADD COMMENT • link updated 14.8 years ago by rgentleman ★ 5.5k • written 14.8 years ago by Barbara Cegielska ▴ 200

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.0 years ago

United States

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- 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

ADD COMMENT • link 14.8 years ago rgentleman ★ 5.5k

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Dear Robert, I was absolutely convinced, that I can ask any question on BioC mailing list...I read many e-mails on the list (R nad BioC), which were asking how to do the data analysis (e.g."OK - I got the data - now what? :-)"). So I felt free to ask... However, I checked the posting guide and I have to admit that I made some mistkes (cross-posting and I was terrorizing the R-help)... I'm not a programmer and I'm still fresh R user, so somethimes it is hard for me to understand something that is obvious for you. I can manage with limma, but GOstats is still extremely difficult for me. My reading list thanks to the BioC mailing list is getting bigger and bigger. I have also ordered "Bioconductor Case Studies" and I'm waiting impatiently... Since I have been using BioC I made progress, so if you don't mind I would like to still use the mailing list. I'll do my best to state my goals and objectives as clear as possible. Best wishes, Barbara

ADD REPLY • link 14.8 years ago Barbara Cegielska ▴ 200

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