yes that would be cool thank you! And regarding the isotopic tracing function I realized that while my parameter file (exported parameters with isotope tracing 13C+15N 'on' is tolerated by the command line application it is also ignored by it. Am I doing it wrong or is this not possible yet?
It is possible to simply export parameters from the MS-DIAl GUI as .txt file which can then be used as parameter-file for the console application (just made a mistake before). The .msdial files which are then exported into the output folder seem to be actual .txt files which could for example be imported into R as such.
I am trying to use the MS-DIAL console application for isotope tracer analysis (lcms-dda). Is this somehow possible? I guess it is not possible to simply use a parameter.txt file that can be exported from the GUI (at least I did not manage)?
I would also like to automatically export csv-files for the unaligned as well as the aligned peaks after the console application finished.
it seems like it is not possible to disable the "fill gaps" option. I have unchecked "gap filling by compulsion" but in the output I still see that gaps are being filled in the "Fill %" variable. Is this intended behavior? If yes is there a different way to disable the fill gaps step?
Peaks_of_all_samples_for_one_found_feature <- getEIC(xcmsSet_object, groupidx = 1183) #in this case the extracted feature is 1183 plot(Leucine, x) #this is the plot.xcmsEIC however, apparently the "xcmsEIC"-part must not be used for that command
I ran into a little a problem and hope someone can help me understanding it.
I used the centWave algorithm of XCMS to detect peaks. That worked generally well. However one of the peaks I found was the one attached. For obvious reasons I looked into it. However, I found the integration indicated by the plot did not match the area given as "into" even close. I extracted the chromatogram to test it and although it looked absolutely the same the area was just different by orders of magnitude. When I tried to find out the reason I saw that rtmin and rtmax confirm the plotted integration boarders. However, scmin, scpos and scmax are all given as -1 which does not really makes sense. lmin and lmax are confirming the values in mzmin and mzmax. Could somebody please explain this to me? I just cant wrap my head around it...
mz mzmin mzmax rt rtmin rtmax into 28945 116.0705011 116.0703547 116.0706169 85.88142934 57.2363598 92.180892 1625626.385 intb maxo sn egauss mu sigma h f dppm scale scpos scmin 1301337.896 7340575 137 0.0340379 335.2332267 2.950305611 7058107.727 56241 0 -1 -1 -1 scmax lmin lmax sample -1 218 351 5
Ps.: I also wonder how the rt is calculated here. It is neither the average between mzmin and mzmax nor at the highest intensity.
Thanks in advance to all the people who are contributing to this forum.
Hello, I would have a question which is very related to the one already asked here. I can manage to plot EICs from grouped xcmsSet objects with something like the code below.
However, I was wondering if this is also possible for XCMS objects before they have been grouped. I would also like to check the performance of the peak integration.
Would be great if someone could help out with that.
Anyway thank you a lot for your time and efforts. Yasin
