fillPeaks(xset_gr) error in xcms

[manasonur]

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

[sneumann]

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