dear ALL: If i have GO annotation file, which R package can be used to do all the statistics and output maps. TopGO? The GO annotation file in such format UN000001 GO:0005515 UN000001 GO:0000741 UN000001 GO:0004252 UN000001 GO:0004176 UN000001 GO:0070361 UN000001 GO:0051131 UN000001 GO:0070407 UN000001 GO:0009507 UN000001 GO:0003697 UN000001 GO:0042645 UN000001 GO:0003727 UN000001 GO:0005829 UN000001 GO:0009560 UN000001 GO:0006515 UN000001 GO:0001666 UN000001 GO:0007005 UN000001 GO:0051260 UN000001 GO:0006200 UN000001 GO:0005524 UN000001 GO:0034599 UN000002 GO:0005515 UN000002 GO:0000741 UN000002 GO:0004252 UN000002 GO:0004176 UN000002 GO:0070361 UN000002 GO:0051131 UN000002 GO:0070407 UN000002 GO:0009507 UN000002 GO:0003697 UN000002 GO:0042645 UN000002 GO:0003727 UN000002 GO:0005829 UN000002 GO:0009560 UN000002 GO:0006515 UN000002 GO:0001666 UN000002 GO:0007005 UN000002 GO:0051260 UN000002 GO:0006200 UN000002 GO:0005524 UN000002 GO:0034599 UN000003 GO:0005515 UN000003 GO:0000741 UN000003 GO:0004252 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Dear Shan Gao, I'd be glad to try to help with this. Could you give us a sense of the biological problem you wish to address? Once I understand that, I can make some concrete suggestions. Best, - Paul > dear ALL: > If i have GO annotation file, which R package can be used > to do all the statistics and output maps. TopGO? > > The GO annotation file in such format > UN000001 GO:0005515 > UN000001 GO:0000741 > UN000001 GO:0004252 > UN000001 GO:0004176 > UN000001 GO:0070361 > UN000001 GO:0051131 > UN000001 GO:0070407 > UN000001 GO:0009507 > UN000001 GO:0003697 > UN000001 GO:0042645 > UN000001 GO:0003727 > UN000001 GO:0005829 > UN000001 GO:0009560 > UN000001 GO:0006515 > UN000001 GO:0001666 > UN000001 GO:0007005 > UN000001 GO:0051260 > UN000001 GO:0006200 > UN000001 GO:0005524 > UN000001 GO:0034599 > UN000002 GO:0005515 > UN000002 GO:0000741 > UN000002 GO:0004252 > UN000002 GO:0004176 > UN000002 GO:0070361 > UN000002 GO:0051131 > UN000002 GO:0070407 > UN000002 GO:0009507 > UN000002 GO:0003697 > UN000002 GO:0042645 > UN000002 GO:0003727 > UN000002 GO:0005829 > UN000002 GO:0009560 > UN000002 GO:0006515 > UN000002 GO:0001666 > UN000002 GO:0007005 > UN000002 GO:0051260 > UN000002 GO:0006200 > UN000002 GO:0005524 > UN000002 GO:0034599 > UN000003 GO:0005515 > UN000003 GO:0000741 > UN000003 GO:0004252 > > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email: > sg839 at cornell.edu > > Facebook: > http://www.facebook.com/profile.php?id=100001986532253

Hi Shan, Here is a good way to get acquainted with Bioconductor's basic GO analysis capabilities: biocLite(c ('GOstats', 'topGO')) library(GOstats) library(topGO) vignette('GOstatsHyperG') vignette('topGO') The two vignettes will be displayed in your default pdf viewer. They should give you a good start on some of our traditional approaches. - Paul On Sep 28, 2012, at 12:29 PM, wang peter wrote: > dear paul: > thank u very much for your help > i have no ideas now > just do some regular analysis to see what special > and generate ideas > > first GO term significance test > then .. > > shan