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Topic: centWave & ROIs (Read 4808 times) previous topic - next topic

centWave & ROIs

Hello,

I am hoping for some clarification on the ROIs generated by centWave and the features ultimately identified after the wavelet step. In particular, can you have one ROI that ultimately ends up being two features?

I think, from reading the Tautenhahn 2008 paper, the answer is yes (see bottom of page 7 of 16), but can someone confirm that?

Thanks,
Krista

Re: centWave & ROIs

Reply #1
Krista,

Exactly right! One ROI can form 2 detected wavelets/peaks. This is due to how the wavelets are able to accurately identify split peaks. Its probably worth turn the sleep parameter on while you do a peak picking so that you can see this as it happens. Of course there might not be any roi's that get split in your dataset.

Since the roi pass is just a rough pass on the data it's not perfectly picking up the individual features. Its just there so that the wavelets have something to work on and so that the data isn't binned.

Hope it helps,
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: centWave & ROIs

Reply #2
Thanks!

Re: centWave & ROIs

Reply #3
Is there a way to save the individual plots? I have been using the manual ROI finding with great success, but now I would like to go one step further and see the results from each wavelet/peak finding step.

The sleep value is helpful. However, there is a tradeoff between wading through lots of figures with a high sleep value, or having them go by too fast in order to get through all of the figures.

In other words, based on some of the downstream analysis, there are specific m/z values and retention times I want to check. However, while I did eventually figure out that I could use scanrange = cbind(#,#) [and not c(#,#)] with findPeaks.centWave, I still have lots of figures to wade through.

Re: centWave & ROIs

Reply #4
Hi,

I haven't checked (just beyond dinner over here)
but you should be able to 1) say pdf(filename)
and dev.off() afterwards to save the plots to pdf.
2) you should be able to par(mfrow=c(10,5)) to place
5 by 10 plots onto one page.

Yours,
Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

Re: centWave & ROIs

Reply #5
This worked:

pdf(file="someFile.pdf")
xs<-xcmsSet( ... )
dev.off()

It seemed to ignore par(mfrow=c10,5)), but that was fine because I end up with a PDF with one page per feature.

Thanks!

Krista