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Messages - kraigkraig

3
XCMS / Re: visualizing SNRthresh
Hi Ralf,

Another novice question:

How do I go about appending the maxo, into, intb, and sn columns to the diffreport?  I tried:
diffreport1 <- diffreport(xset,"class1","class2",eicmax=300,eicwidth=200,value=c("into","maxo","intb"))
This gives the diffreport without errors, but does not add columns.

K :(
4
XCMS / Re: visualizing SNRthresh
Wow, there sure is a lot to learn about this great software.  Setting sleep=2 made for a fairly painful slideshow, but it does accomplish what I was looking to do.
Do you recommend the use of Gaussian fitting to eliminate bad features? 

Thanks for answering my novice questions...

Kraig
5
CAMERA / Re: annotation of doubly charged metabolites
Hi,

I have a question along the same lines.  Does CAMERA use the intensity of the masses when assigning an isotope group, or just the the masses/retention time?  I have encountered a situation where the M+ is assigned to a mass that is 10000x less intense than the real M+1 of a known compound.  It may be an elimination product of the parent M+H that co-elutes or an artifact.  A picture:



Is there any way to prevent wrongly assigning isotopes by considering peak intensity? I'm not sure if this is in the scope of what CAMERA does.

Thanks, I hope this is clear as mud!

Kraig Worrall
6
XCMS / visualizing SNRthresh
Hi,

Recently I have been toying around with setting a sensible signal-to-noise threshold. I have a data set where the concentration of the samples was excessive.  The chemical noise of these samples is high, but the data seems usable (I hope). I would like to set the filter in such a way that reliable peaks are conserved and noise is reduced, but I'm not sure of the best way forward. 

Is there way to visualize the outcome of the SNR-threshold on the raw data on a known peak?  Is there a good way to set this criteria in a non-arbitrary manner?  I may be missing some more obvious or graceful solution, so I would appreciate any input!

Cheers,

Kraig Worrall    :|
9
XCMS Online / snrthresh & chromatogram cropping
Hi,

First time poster here! I have two questions about XCMS online.  :?:

First, is it possible to adjust the signal-to-noise threshold with XCMS online?

Is it possible for me to crop sections of the chromatogram so that signals from unwanted regions will not be tabulated?, e.g. first minute and column wash out.

Thanks,

Kraig Worrall
Agriculture and Agri-foods Canada