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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Baseline Correction #317

Closed Gronnesby closed 5 years ago

Gronnesby commented 5 years ago

I can't seem to find any mention of baseline correction in the XCMS documentation.

I saw some mention of centWave performing baseline correction as part of peak detection (paper), but is there any way to explicitly calculate a baseline for a given spectra?

jorainer commented 5 years ago

Nope, xcms does not do any baseline correction (apart from the baseline estimation in centWave). It would also make more sense to have such a function/method in a lower level package (such as MSnbase).

Unfortunately there is no such function available there (yet) - I've however spotted a baseline correction function in the MALDIquant package, so eventually @sgibb could chime in here?

sgibb commented 5 years ago

MALDIquant offers 4 different baseline estimation/correction algorithms (but of course they were written/selected with MALDI in mind): https://github.com/sgibb/MALDIquant/blob/99fe5a3f269881f7aac76acc70a6a17b4e767a98/R/estimateBaseline-functions.R#L13-L31

We could simply offer this functionality through MSnbase as we have done with smoothing and peak detection. If you think it is useful I could do this.

sgibb commented 5 years ago

BTW: there is also a baseline package on CRAN (but all its methods are written in R and most of them require a matrix with fixed mz values (= same mz for all spectra, which was useless in our MALDI experiments) and intensities). If there is a special algorithm of interest in this package we may need to reimplement it in C/Rcpp.

Gronnesby commented 5 years ago

I don't really have a pressing need for a baseline correction method, I have been using AirPLS (https://github.com/zmzhang/airPLS) so far, which works quite well. It was more out of curiosity if XCMS implemented their own baseline correction method that I could compare to. Thanks for the clarification.