Hi,
I just got the results of my first XCMS online analysis and it worked like a charm. I have two question about the presentation of the results in the results table:
1) In the "feature group" features with very different retention times are assigned to the same feature group. e.g. a particular feauture group contains features with retention times ranging from 16 to 51 minutes. How is that possible? I thougth that one of the criteria to be grouped in one feature group was that the features should have the same retention time.
2) to what do the numbers between the square brackets [] in the column "isotopes" refer?
Koen
Thank you for reporting the problem, it seems that there is something going wrong with the feature grouping for that dataset.
I'll look into it.
XCMS-Online uses the CAMERA package for feature annotations.
The number in square brackets in the column are used to indicate features, that 'belong together'.
e.g. [14][M]1+ would be the 12C peak, [14][M+1]1+ the 13C peak, singly charged.
[14] itself doesn't mean anything, it is just a consecutive number for this group of isotopic peaks from the same metabolite.
Also see the CAMERA user manual http://http://bioconductor.org/packages/2.9/bioc/vignettes/CAMERA/inst/doc/CAMERA.pdf
The feature group problem is fixed now.