> My question is, if I need to compare between 5 time points, should I do > comparison pairwise?
No, do them all at once with Cuffdiff: (a) set 'Perform Replicate Analysis' to 'Yes'; (b) create 5 replicate conditions, one for each time point; (c) add your replicates for each time point. There's a Cuffdiff flag to do time series analysis, but it isn't implemented yet in Galaxy, so you'll get pairwise comparisons for all conditions. You can use the filtering tool to reduce Cuffdiff outputs to only the timepoint comparisons. > I will use cuffmerge to merge 0hour-1, 0hour-2, 0hour-3, > 1hour-1,1hour-2.1hour-3 to generate one cuffmerge file. Correct. > Then I will run cuffdiff using the merged file, include two groups, group 1 > is 0 hour (add 0hour 1-3 in group 1) and group 2 is 1hour (add 1hour1-3 in > group 2). Use the process I described above to do all pairwise comparisons in one run. Good luck, J. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
