Peak width error while trying to identify peaks using centWave

November 15, 2017, 10:09:37 AM

Hi all,

I have been trying to pick peaks using the centWave method in xcms. This is for tissue samples analysed using the Waters UPLC-qTOF. The error I see after the very first step is as follows:
Error in .local(object, ...) : No scales ? Please check peak width!
And a warning message as follows:
Warning message:
In xcmsRaw(arg$file, profmethod = params$profmethod, profparam = params$profparam, : There are identical scantimes.

The script I have used is M1 <- xcmsSet(cdffiles, method="centWave", ppm=20, peakwidth=c(5,60), snthresh=10, prefilter=c(3,100), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=F) which is based on the chromatogram I see and has worked for me before. I tried playing around with different peak widths, and still see the same error message. Can anyone help me with what's going on and if there is any other parameter I should be changing?

Thank you!
Anuri

Re: Peak width error while trying to identify peaks using centWave

Reply #1 – November 15, 2017, 12:39:25 PM

Perhaps a bad file? https://github.com/sneumann/xcms/issues/55

Re: Peak width error while trying to identify peaks using centWave

Reply #2 – November 18, 2017, 06:44:12 AM

Thanks Jan, it worked with a new file.