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XCMS / centWave warning of not centroid mode data
xcmsSet(mzXML.files, snames = snames, sclass = sclass, method = 'centWave', ppm = 10, peakwidth = c(20, 50), snthresh = 10, prefilter = c(3, 1000), integrate = 1, mzdiff = -0.001, verbose.columns = TRUE, fitgauss = FALSE)
Out of 167 samples, 15 gave the the following waring
In .local(object, ...) :
It looks like this file is in profile mode. centWave can process only centroid mode data !
What are the possible reasons?
What are the consequences on the following steps?
I found that retcor didn't work with the following error message: (after group)
"No peak groups found for retention time correction"
Details:
> xset <- group(xset)
262 325 387 450 512 575 637 700 762 825 887 950 1012 1075 1137 1200
> xset.retcor <- retcor(xset, family = 'symmetric', plottype = 'mdevden')
Error in .local(object, ...) :
No peak groups found for retention time correction
> traceback()
8: stop("No peak groups found for retention time correction")
7: .local(object, ...)
6: retcor.peakgroups(object, ...)
5: retcor.peakgroups(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: retcor(xset, family = "symmetric", plottype = "mdevden")
1: retcor(xset, family = "symmetric", plottype = "mdevden")
> dim(xset@groups)
[1] 2990 9
We can see that the groups element is not empty.
Any ideas? Many thanks.
Bowen