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Topic: Generating centWave Images(from Ralf's Bioinformatics paper) (Read 1501 times) previous topic - next topic

Generating centWave Images(from Ralf's Bioinformatics paper)

Hello

I am interested in generating the images from Ralf's Bioinformatics paper in 2008 (Highly sensitive feature detection for high resolution LC/MS).  Specifically pages 5,9 and 10 of the m/z domain and the corresponding chromatogram with applied wavelet. If anyone has done this before, I would greatly appreciate a point in the right direction.

Can I extract this data from R as the algorithms are being applied, or will I need a separate software for this generation?

Thank you again-
Ashley Sidebottom

Re: Generating centWave Images(from Ralf's Bioinformatics pa

Reply #1
Have you tried using the "sleep" option for centWave which will generate similar visualizations ?

By using something like 
Code: [Select]
pdf(file="myplots.pdf")
xcmsSet(method="centWave", sleep=0.0001,...)
dev.off()
you can save the plots to a pdf file.

To enable the Gaussian fits, turn on "fitgauss=TRUE".

Re: Generating centWave Images(from Ralf's Bioinformatics pa

Reply #2
Is there some way to limit what m/z range you get when you do this? I would like to see the Gaussian fit for a particular compound where I know, based on the peakTable, the m/z and RT; how do I do that?