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XCMS / Re: XCMS and fast polarity switching
i have data with fast polarity switching mode from Thermo Exactive and Q-exactive,first i converted in proteowizard using pickpeaking filter( for centroid data), the i try to process the data with' polarity="positive"and" negative",but it seems the result is the same. here is the scrips:
Code: [Select]
XMLfiles=list.files(path=".", recursive=TRUE, pat="mzXML")
>
> xset1=xcmsSet(XMLfiles, method='centWave', ppm=5, peakwidth=c(5,12), snthresh=5, polarity="positive")
xset1=group(xset1)
xset1=fillPeaks(xset1)
xset2=xcmsSet(XMLfiles, method='centWave', ppm=5, peakwidth=c(5,12), snthresh=5, polarity="negative")
xset2=group(xset2)
xset2=fillPeaks(xset2)
but xset1 and xset2 show exactly the same result. matchedfilter was also used on data without peakpicking in proteowizard , but it also showed no difference between 'polarity="negative"and "positive" '
and it's the latest version of xcms. Seek for help!
If this method not work, how to use split() ? what is the parameters?
Thanks
yaoyao