Dear XCMS community,
I have noticed that the number of feature groups in my xcmsSet object after running fillPeaks is generally (always?) less than the number that existed immediately after grouping. Evaluation of the data reveals that the groups appear to be deleted outright - and the features that were in that group can not be found in any other group. To my eye, these removed groups are not special or outstanding in any way. I typically use "nearest" grouping, and have not yet seen this problem when using "density" grouping.
Has anyone else observed this behavior? Does anyone know why this happens?
Where are the peak groups going!?
thanks,
m