hi there, I've generated the bingo files (GO enrichment tests) for those runs, they are in: /group/biocomp/projects/segal/erbon/ath_20071023_bingo_results Steven, I've used the file A_thaliana_ORF_TAIR_230606 which might not be the latest one? -- Eric Tom Michoel wrote:
Hi,
With the latest LeMoNe code and no other jobs running on tornado, 4 runs were finished in about 5 days.
Now we need some basic analysis to see if anything cell-cycle related is showing up ... then we can play with some parameters to see how they affect results.
For the experienced people, the output is here:
/group/biocomp/projects/segal/tomic/LeMoNe/results/Arabidopsis/20071023
xml/ : use -Xmx7000m to read these figs/ : figures for all modules, separated for each of the runs figs2/ : figures ranked by edge weight (using "max") figs3/ : figures ranked by edge weight (using "sum")
20071023_edges_max_ranked.txt, 20071023_edges_sum_ranked.txt : networks ranked by edge weight (using both ways to compute edge weights)
20071023_edges_1000.cys : cytoscape file with best 1000 edges for both networks
moduleSet_##.txt : gene clusters for each run.
Tom