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fillPeaks(xset_gr) error in xcms #72

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manasonur opened this issue Aug 28, 2021 · 1 comment

manasonur commented Aug 28, 2021 •

edited

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datapath <- ("C:/Users/onur/Desktop/emrah")
datafiles <- list.files(datapath, recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(datafiles, method="centWave", ppm=18.5, peakwidth=c(6,24),

            prefilter=c(3,2000), snthresh=10, fitgauss=FALSE,

            mzCenterFun="wMean", integrate=1, mzdiff=0.01, noise=5)

Detecting mass traces at 18.5 ppm ... OK
Detecting chromatographic peaks in 16187 regions of interest ... OK: 7653 found.

xset_gr = group(xset)
Processing 11537 mz slices ... OK
xset_fill <- fillPeaks(xset_gr)
Error in matrix(nrow = nrow(gvals), ncol = 4) : non-numeric matrix extent
I get a error like above and could not figure out. Could you please help me for that
Thanks
Onur

The text was updated successfully, but these errors were encountered:

Owner

sneumann commented Sep 6, 2021

Hi, sounds like an xcms issue rather than CAMERA.
Please provide operating system, version(s) of R and xcms.
In addition, I would recommend to use the new xcms3 interface described in http://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
Yours, Steffen

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