On 29/11/13 04:31 PM, JC Grenier wrote: > Hi Sebastion, Hi,
> > I'm communicating directly with you cause I have a figure to show you > concerning some analysis that I'm doing with GO terms. I >looked into the different depth just to see if I can see some difference >between both groups that I'm working on and found some weird stuff. > You should use Terms.tsv or Terms.xml because those for specific depths are not accurate because of mainly 2 reasons: 1. EMBL_CDS sequences are annotated with any GO term, not just with leaves in the GO classification 2. The GO classification is directed acyclic graph, but a GO term can have many parents. The depth files use recursive counts, whereas Terms.xml/Terms.tsv don't. In our paper, we used the most abundant terms from Terms.xml regardless of depth. ( http://genomebiology.com/2012/13/12/R122/figure/F5 ) This was discussed before on https://github.com/sebhtml/ray/issues/158 and on http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/406 P.S. the files for depths will likely be removed at some point. (see # 158). > I took my results from the file Terms.tsv. > > Here's one example. Can you tell me why this pattern exists? I don't understand what you expect me to see here. Perhaps it would be wise to draw 1 colored line per sample. >Like all the dots aligned (first why are they aligned...?) are from the same >sample? Is this a coverage or number of reads artifact? The proportions are computed in terms of k-mer observations divided by total number of k-mer observations. So I don't think it is necessary to normalize here since they are relative numbers. > > Thanks a lot for your help > > -- > Jean-Christophe Grenier, M.Sc. > > ----------------------------------------- > /Bio-informaticien/ > /Laboratoire de Philip Awadalla/ > /Laboratoire de Luis Barreiro/ > /CHU Sainte-Justine/ > //3175, Côte Sainte-Catherine, local B-607 > ///Tél : 514-345-4931 poste 5199/ > ----------------------------------------- ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
