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Topic: Bad peaks detection (Read 4115 times) previous topic - next topic

Bad peaks detection

Hi All,

I had a look to the plot generated by the FindPeaks function using this code:

Code: [Select]
pdf("peaks.pdf")
a <- xcmsRaw("120630_Pivus_000401.CDF")
b <- findPeaks(a,"120630_Pivus_000401.CDF", method = "centWave", ppm=25 , peakwidth=c(2:15), snthresh=12, mzCenterFun="wMean", integrate=2, mzdiff=0.05 , prefilter=c(1,5), sleep=0.0001, fitgauss=T)
dev.off()

Peaks in general seem well detected except for few of them:

[attachment=0:wwrp9gac]bad_peaks.pdf[/attachment:wwrp9gac]

Do you have any explanation of what is going wrong in these peaks detection? Shall I change some parameter to avoid this problem?

Thanks!

Best,

[attachment deleted by admin]