XCMS_demo课件.ppt

This tutorial uses the FAAH data, downloaded from the XCMS homepage (/download/) to lead the user through each step of xcms. 7 simple commands for one complete XCMS data analysis library(xcms) xset - xcmsSet() xset - group(xset) xset2 - retcor(xset, family=s, plottype=m) xset2 - group(xset2, bw =10) xset3 - fillPeaks(xset2) reporttab - diffreport(xset3, WT, KO, example, 10, metlin = 0.15);Open R, load xcms User input is shown in red;Go to File toolbar at the top of R, choose Change dir…, and select the folder containing the .cdf files;Upload data files completed;Check loaded data; this step is optional and does not affect data analysis.;Group peaks (without visualization);Or add sleep = .001 to the group command for grouping peaks with visualization;Grouping shown as plots;The retcor command can either be typed out completely i.e. using family = “symmetric”, plottype = “mdevden” or simply as family = “s”, plottype = “m”. Note: the object name ‘xset2’ is used here, so that the original xset will not be overwritten.;Regroup data after retention time correction;Fill in with original data where peaks were not detected initially. Note: the object name xset3 is used here, so that xset2 and xset will not be overwritten.;Check current data status; this step is optional and does not affect data analysis.;Create report: “WT” and “KO” denote the class names of the data sets being compared “example” is a user defined output file name for the spreadsheet report 10 is a user defined number of extracted ion chromatograms (EIC) that will be plotted metlin = 0.15 specifies the m/z tolerance for potential metabolite matches from the METLIN database;Both the EICs and spreadsheet report (as a TSV file) are created in the same folder where the raw data are stored;Inside the EIC folder. EICs can also be visualized in many picture viewing programs;Spreadsheet “example” opened in Excel;Type ? before the function name to retrieve documentation immediately i.e. ?retcor will