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Messages - gunnar

1
XCMS / Re: memory error during fillpeak step
fillPeaks seems to loose all values except mz, mzmin, mzmax, rt, rtmin, rtmax, into, maxo and sample.

Is this somehow related to R3.0?

any solutions?

br
Gunnar
2
XCMS / Re: fillPeaks produces high intensities
Hello Ralf,

we had a closer look into the raw data and may have found the origin of the problem:

Measurements were made with a LC/FTICR-MS system (LC coupled to  Thermo LTQ FT Ultra) which produces data with quiet a high resolution. In the raw-files with the high intensities is a very small peak, therefore not found by findPeaks. Unfortunately nearby (~60ppm and same RT) is a high peak which is later filled in by fillPeaks. That led to the clue that the step-width of fillPeaks was to wide. Since step is taken from the xcms-object we added
profparam = list("step" = 0.01)
to the xcmsSet-parameters.
Now fillPeaks looks in a more narrow mz-slice and, as far as we can say, chooses the right peak.

best regard

PS:
that also benefits EIC-diagrams which are more accurate now :-)
3
XCMS / fillPeaks produces high intensities
Hello!

I was wondering if fillPeaks always calculates the right intensities. Here an example:

[attachment=0:1pmk1zva]findPeaks.png[/attachment:1pmk1zva]

[attachment=1:1pmk1zva]fillPeaks.png[/attachment:1pmk1zva]

The peak is correctly identified by fillPeaks but the intensity is to high compared to the peak from findPeaks.

sessionInfo:
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=de_AT.UTF-8      LC_NUMERIC=C             
 [3] LC_TIME=de_AT.UTF-8        LC_COLLATE=de_AT.UTF-8   
 [5] LC_MONETARY=de_AT.UTF-8    LC_MESSAGES=de_AT.UTF-8 
 [7] LC_PAPER=C                LC_NAME=C               
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C     

attached base packages:
[1] stats    graphics  grDevices utils    datasets  methods  base

best regards
Gunnar

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4
XCMS / Re: how to get RT-Values for a peak
Hello!

I think the simple way is just fine for me, since i also need raw and corrected rtmin and rtmax values.
Thanks for your help.

Gunnar
5
XCMS / how to get RT-Values for a peak
Hy all!

How do I get rtmin and rtmax values (raw as well as corrected) for a specific peak? I know that there are columns for rtmin and rtmax in xcmsSet@peaks. Are those raw or corrected RTs? I also know that there are xcmsSet@rt$raw and xcmsSet@rt$corrected values but I dont know how to link those values to a peak neither how to get rtmin and rtmax from those values. It also seems that in xcmsSet@rt are less values than peaks.

As for xcms settings I build the xcmsSet as follows:
xset <- xcmsSet(...)
xset <- retcor(xset, method = "obiwarp")
xset <- group(xset,...)
xset <- fillPeaks(xset)

Thanks
Gunnar
7
XCMS / fillPeaks and sn-values
Hy all!

I have a question regarding fillPeaks(). Do the intensities coming from fillPeaks have a SN-value of NA?
I'm asking because when I look at my data I have a lot of NA's in my SN column and I want to avoid them since the method xcmsSet should identify most of my peaks. When I look at the EIC-diagrams there are very clear peaks but a lot of them come (as I think) from fillPeaks and not from xcmsSet-method.

I'm using the following parameters:
xset <- xcmsSet(method='centWave', ppm=15, peakwidth=c(30,120), snthresh=100, prefilter=c(3,10000), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=TRUE, verbose.columns=TRUE, nSlave=4)
Second question would be: Which parameters should i change to get more Peaks from xcmsSet or to get more SN-values which are not NA?

br
Gunnar

PS: We are using a LTQ Orbitrap XL for analysis

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