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Topic: CDF chromatogram alignment (Read 220 times) previous topic - next topic

  • vso
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CDF chromatogram alignment

I have a series of chromatograms (as CDF files) that I want to align and re-export them to CDF. Is this possible with any of the free software like XCMS?

Thanks in advance

  • Jan Stanstrup
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Re: CDF chromatogram alignment
Reply #1
Would be possible with some hacking, yes. The CDF writer in XCMS is not compatible with any other software though. If you can use one of the XML based formats it is more feasible.

I think what you'd need to do is do peakpicking, feature grouping and retcor. Then use the results from retcor to modify and xmcsRAW object with the corrected retention times.
You will only change the scan times this way though. You won't get any fancy peak warping.

You might want to take a look at MSnbase for handling the raw data. The development version of XCMS uses MSnbase-based handling of the raw data.
  • University of Copenhagen, Denmark

  • vso
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Re: CDF chromatogram alignment
Reply #2
Thanks Jan, found the code here ( - thanks to Agne). Modified the XCMS parameters for single quad data and removed the fillPeaks step. Compared aligned with raw and it seems to work just fine.