centWave - help

October 04, 2011, 05:09:12 AM

Hey everyone,

I have some cdf files of HPLC-MS samples. Sometimes, when I try the centWave algorithm I get the error message SIZE_PEAKBUFS too small !
I think it is because the file is in profile and not centroid mode. Can anyone confirm this? The problem is that most of my samples are in centroid mode, but I suspect a few might be in profile...

Also, when I try using parameters like this, which I see everyone mentioning here in the forum (this example was posted by hpbenton on another centWave related thread)
xr<-xcmsRaw(file, profstep=0
peaks<-findPeaks.centWave(xr, snthresh = 10,ppm=3,prefilter = c(3,150),peakwidth=c(5,60),mzCenterFun="wMean",integrate = 1,fitgauss= TRUE,noise = 100)

I get the unused arguments error... Shouldn't it work right away?

Thanks in advance

Re: centWave - help

Reply #1 – October 04, 2011, 09:07:09 AM

It seems like the XCMS version you are using is outdated.
Please upgrade.

Re: centWave - help

Reply #2 – October 05, 2011, 06:30:10 AM

Although my xcms version was the latest, I was using a previous version of R, but now after the update everything seems fine.

Thank you!