I have the same problem as many people have had, and I found posts relevant to this topic but was not able to get the code to work. So I have HILIC UPLC-MS data. I tried running xcms but received this error saying that m/z sort assumption was violated. I tried running the following code but I got no output and no .CDF files were corrected; can you please advise me on what I should do next:
## Notes: This program will check the m/z vector for a single file for sort violation ## If a sort violation is found the m/z vector is reorganised along with the Intensity ## vector. Finally a new CDF file is made which is fixed. ## !!!NB!!! : Parallel version does not report progress
it has been a while since I posted. I just have a quick question regarding the "minPtsAboveBaseLine" option, and if it is available for tweaking in the online XCMS version at this time? This is important for some features I would like to be able to extract using XCMS.
Yup, that is what I used and I don't believe it is oversaturated. I am having this issue with some of our masses of interest not being extracted but they are when I use Mass Lynx. I don't understand XCMS well enough yet to be able to "intelligently" tweak parameters, but I have tried playing with them..but still nothing in terms of getting the masses I am interested in.
I played with parameters and set s/n=5, but still nothing, I cannot get the mass to come through in XCMS. The peak looks normal, yes! That particular mass has relatively abundant counts in 30% of samples. So it really should be coming through.
I really don't know what other parameters to tweak so that I can get it to come through? Any suggestions?
sorry I never saw that you posted this reply back in May. I am still having the same issue with a mass not being extracted in XCMS but it does come through using Mass Lynx.
The instrument we are using is UPLC-ESI-QTOFMS. Can you tell me please what XCMS parameters you think I should try to tweak in order for cotinine to come through?
I am trying to use some stored datasets for a new job I am creating, but only when I click on Data 1 "select stored dataset" does it show me my stored datasets. Data 2 shows that I have no stored datasets--is this a bug?
Thanks so much for your reply, and your answer definitely helps.
My parameters are already set so that I can capture as much stuff as possible. When I use Marker Lynx, my ion comes through. So if I were to change signal/noise threshold (which is currently set at 10) what do you suggest I put it at?