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Title: CDF chromatogram alignment
Post by: vso on February 19, 2018, 12:43:53 PM

Hello,

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

Title: Re: CDF chromatogram alignment
Post by: Jan Stanstrup on February 19, 2018, 01:16:24 PM

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.

Title: Re: CDF chromatogram alignment
Post by: vso on February 20, 2018, 09:40:40 AM

Thanks Jan, found the code here (http://www.metabolomics-forum.com/index.php?topic=842.0 - 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.

Metabolomics Society Forum

Software => Other => Topic started by: vso on February 19, 2018, 12:43:53 PM