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XCMS Analyte Profiling Software Tutorial. This tutorial uses the FAAH data, downloaded from the XCMS homepage ( http://metlin.scripps.edu/download/ ) to lead the user through each step of xcms. 7 simple commands for one complete XCMS data analysis library(xcms) xset <- xcmsSet()

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xcms analyte profiling software tutorial
XCMS Analyte Profiling SoftwareTutorial

This tutorial uses the FAAH data, downloaded from the XCMS homepage (http://metlin.scripps.edu/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)

slide2

Open R, load xcms

User input is shown in red

slide3

Go to File toolbar at the top of R, choose Change dir…,

and select the folder containing the .cdf files

slide4

Upload data files

xset is a user defined object name

Upload data files completed

slide9

Retention time correction

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.

slide11

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.

slide13

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
slide14

Both the EICs and spreadsheet report (as a TSV file) are created in the

same folder where the raw data are stored

slide15

Inside the EIC folder.

EICs can also be visualized in many picture viewing programs

slide17

Type ? before the function name to retrieve documentation immediately

i.e. ?retcor will bring up the retention time correction documentation page.

slide18

All the functions and classes are documented and are available from R under Help > Html help > Packages > xcms.