xcms documentation August 16, 2011, 06:56:03 AM Hi,first I have to say that I just started using R, I tried to find some answers in thisforum but did not succeed.I am looking for a documentation of the different methods for feature detectionand their parameters. Further I do not understand all columns in the peaks table after peak detection:mz, mzmin, mzmax, rt, rtmin, rtmax and sn are self explaining. But what dointo, intf, maxo, maxf, i and sample mean ?Regards, Uwe Quote Selected
Re: xcms documentation Reply #1 – August 16, 2011, 08:30:53 AM Hi,R has some extensive documentation in form of manual pages,they take a bit to get used to, but are well structured. Check e.g. help("findPeaks.matchedFilter") or help("findPeaks.centWave").Also, check the papers for more on the algorithm: Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006) Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)Hope that helped,Yours,Steffen Quote Selected