Hi guys, have a question about the cuffdiff output "differential expression testing".
For most of you might sound "naive" but I'm new to this field and I have very little background in statistic. So, I have compared a control sample with 2 biological replicates using cuffdiff. I have now about 4000 genes which were tested. 1. How do I extrapolate the genes which are up- or downregulated from the 4000? 2. Is there a FPKM value above which a gene is up- or downregulated? 3.I used excel and sorted the values from highest to smallest: assuming that control highest value is 200 and the correspondent treated values is 2, can I say that that gene is downregulated in the treated ssamples by a 100 fold chnage? 4. Do I have to use at all the p_values given in the output to extrapolate the most up- or downregualted genes? I do not have yet cummerbund and I am not very good with R. And I 'm lost! Thanks, ib ___________________________________________________________ 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/