Hi Diego, The various labs calculate the data and submit it to us. We recommend that you contact the lab that submitted the data for a more detailed information on how they calculated it. The lab contact information is located on the track description pages.
If you have further questions, please contact the list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Diego Pereira <[email protected]> Date: Tue, Feb 7, 2012 at 11:41 AM Subject: [Genome] Fwd: pValues and Score fields To: [email protected] Dear Vanessa, Thanks for your reply. Yes I read that in the schema of the table. However, by performing the following exercise: For a signalValue = 8.01812 pValue = -log10(signalValue) -LOG10(8.01812) =-0.904072552 pValue = -0.904072552 which is different than the reported pValue. pValue=15.4 Excuse me if I'm doing the math in the wrong way. If so, how should I do the math? On the other hand please let me know if the score fields are useful for statistical analysis. Regards, Diego El día 7 de febrero de 2012 14:18, Vanessa Kirkup Swing <[email protected]> escribió: > Hi Diego, > > The reason you are seeing high numbers for the pValue is because we > use -log10. More information about ENCODE file formats can be found > here: > > http://genome.ucsc.edu/FAQ/FAQformat.html > > and additional information can be found by clicking on the "schema" > links for each track in the track description pages. > > Hope that clarifies the issue for you. If you have further questions, > please email the list: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Diego Pereira <[email protected]> > Date: Tue, Feb 7, 2012 at 5:46 AM > Subject: [Genome] pValues and Score fields > To: [email protected] > > > Good morning, > I'm wondering, what is the meaning of those pValues of 3100, 324 etc? > How do they are calculated? > I never saw something like that before. > I usually think about pValues as quantities in the range from 0 to 1. > So those values confuse me a little bit. > On the other hand, how useful are your score fields for statistical purposes? > I understand the primary use of those fields is for the graphics. > However, it seems they are "normalized" data, so I'm wondering whether > I can use them saving me to reinvent the wheel. > Regards, > Diego > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
