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.