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Topic: Export signal to noise ratio for each peak (Read 4266 times) previous topic - next topic

Export signal to noise ratio for each peak

Hi,
when I run findPeaks.centWave for a single sample I have 

sample@xcmsSet@peaks[1,]
      mz    mzmin    mzmax      rt    rtmin    rtmax    into    intb
883.9883 883.9843 883.9926  3.4120  2.0610  4.7630 788.7590 786.0570
    maxo      sn  egauss      mu    sigma        h        f    dppm
321.0089 320.0000      NA      NA      NA      NA 136.0000  9.0000
  scale    scpos    scmin    scmax    lmin    lmax  sample
  4.0000  3.0000  1.0000  7.0000  1.0000  5.0000  1.0000


and I can access the signal to noise ratio (sn), but for multiple samples it is not present

psample@xcmsSet@peaks[1,]
          mz        mzmin        mzmax          rt        rtmin        rtmax
  83.057046    83.057007    83.057068    1.829970    0.333661    6.427780
        into        maxo      sample
22459.443811  4354.406250    1.000000


is there an average or a combined value that I can export?

thks
 

Re: Export signal to noise ratio for each peak

Reply #1 –
Using the grouping information (indices) from the group'ed xcmsSet, you can simply pull out all the values you need from the full peak matrix and calculate the S/N statistics for each feature as needed.