I am using xcms + camera for metabolomics analysis. After get the "annotated diffreport" file from camera, what should I do next for the database search? How to consider the "isotope" and "adducts" columns that generated by CAMERA?
Recently I found the XCMSonline has some other ways to calculate the fold change, not just mean1/mean2. For example, in the demo COKE vs Pepsi, the 17th record in the diffreport table. The fold change of that record is 7.235695, however, the mean of dataset2 is 0. I suppose there must be another way to calculate such kind of fold change. Can anyone tell me related method? Thanks
Recently I found the XCMSonline has some other ways to calculate the fold change, not just mean1/mean2. For example, in the demo COKE vs Pepsi, the 17th record in the diffreport table. The fold change of that record is 7.235695, however, the mean of dataset2 is 0. I suppose there must be another way to calculate such kind of fold change. Can anyone tell me related method? Thanks
I am using XCMS for metabolomics analysis. The raw data is from UPLC+QTOF machine. When I use the centwave method and set the ppm as 30, the software always show me the warning: "There are 5533 peak data insertion problems. Please try lowering the 'ppm' parameter." Which range should be suitable for the ppm in UPLC+QTOF?
And for the diffreport, after the t-test, do we still have all the data or it's already been cut off by a default threshold?
When perform the annotation, can I just use the values in "mzmed" column with considering proton mass and delta mass? Do I need to calculate isotopes and different adducts?
