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
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?
I am trying to look at a particular mass that I know is in raw chromatograms but for some reason cannot extract it with the parameters I am putting in. I am able to extract it using Marker Lynx software, however.
I am unsure of how XCMS extracts ions and I would really like to understand it. For example, when the instrument takes snap-shots while running samples, one ion can come at several different masses which are a little different (under the same peak) i.e. 107.1043, 107.1057, 107.1068, etc. When XCMS extracts these ions, does it consider them separate or one and the same ion?
I need to have median peak area for something and was wondering if the results file we can download upon running data has that information? If not, is there a way for me to obtain that information?
The last couple of days I have been having problems with data uploads. For some reason, each time I upload there is a different file that has a status of "Invalid MD5". Is there a way to fix this so that all the files get uploaded correctly?
I ran some ESI- data for the first time. I chose negative polarity in the settings, and didn't select any adducts under identification since there were none to choose from. However, the results table still shows positive isotopes i.e. [3][M+1]+ Is there a mistake?
p.s. job ID is: 3543
I also realized it is very possible I am reading the adducts incorrectly. Can you please explain to me what this means, what it refers to: [3][M+1]+
I would like to set mzdiff to -0.005. However, the filed seems to only accept 5 characters, so if I want the value to be negative, the smallest number I can put in is -0.01.
Is there a way to increase the filed so that it fits -0.005?
I tried processing two datasets previously used with different parameters (and the extraction worked that first time). However, this second time around, there is an error saying "XCMS Processing Failed". The only thing I changed in the parameter settings is no retention time.
I am trying to rerun some analysis with different parameters. I have uploaded these datasets before and they went through the file check just fine. This time I am getting an error and the process is stuck at the "file check" point. Job ID is 1898.
Also, is it possible to get more space on the web-based XCMS page?
1. There is a problem I don't know how to fix, and this has happened to me a few times now. I ran some data on XCMS online, and Total Ion Chromatograms (original) does not show any peaks, while the corrected graph looks fine.
The ID of the job I ran is 1799.
Can you please help me fix this?
2. Additionally, I am still unable to change any parameters on UPLC/MS without having an error message pop up saying that min peak width has to be less than the max peak width, and so I cannot save the changes.
I am trying to run my data without a retention time correction so that I can compare data before and after the correction. However, whenever I run the data, an error message appears half way into the run.
1) Am I supposed to be setting up some specific parameters not related to the retention time parameters, i.e. feature detection "method" or "integration method" under feature detection? Are these parameters supposed to be something specific for LC/MS data?
2) Also, I would like to be able to change min peak width and max peak width to 5 and 12, specifically, as I am trying to reproduce some data and follow someone else's foot steps for this particular analysis.
Thank you very much! I appreciate your responses! I am new to XCMS but I am very excited about it, and looking forward to using it more and more!
