Hi Jan, Thanks for the reply and the note about the post moderation. I suppose that makes me a long time lurker/first time poster. In my experience, any example processing using nearest/fillPeaks will lead to the same outcome. This is why i'm interested in whether anyone else has seen this. I see it all the time. I'm happy to peakpick some files and upload the .RDA file, if that's what you mean by post an example. As for why i use nearest - personally, I don't like the concept of density-based grouping, especially when the bin-width is such a non-intuitive parameter. More to the point, i don't like that it is able to (and often does) group peaks together from the same sample, leading to npeaks># samples. I understand that at some point in that process, one of the (potentially) multiple peaks extracted from the sample is selected as the "best" one, but i'm not sure how that selection is controlled. I much prefer - conceptually - the idea of matching peaks using a scoring system, one per sample. It is my experience with synthetic datasets that this gives much more accurate results than density-based grouping. For high res (UPLC) data, the density method really seems to butcher things. Thanks for taking the time to read and respond - much appreciated. matt
Hi Randi, I was wondering the same thing! This board looks very active for issues related to XCMS, but not so much for general analytical chemistry. If anyone knows of active communities for these topics, i'd love to know about them! matt
Hi all, When using the "nearest" grouping method followed by fillPeaks, i find that my xcmsSet object has less groups following fillPeaks than it did just after grouping. The peaks in these groups are not sorted into new groups - they're just gone from the dataset. I've investigated this and can find no pattern in the feature groups that would help explain why fillPeaks deletes them. Has anyone else noticed a discrepancy in the number of groups before and after using fillPeaks? Thanks, matt note to moderators: this is my third time trying to post this question. Please let me know by PM if there is some reason why this keeps getting moderated out! Thanks!!
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
Dear all, I have noticed that my grouped dataset (using the "nearest" method) generally contains more feature groups than the grouped dataset after running the fillPeaks function. I thought perhaps fillPeaks was doing something clever regarding re-grouping, but after inspection, some groups just appear to be gone, and the peaks that were in them are no longer represented in any group, although they are still in the peaklist. I have checked this by confirming that after nearest grouping, all peaks in the dataset are accounted for in groups, however this is not true following fillPeaks. Can anyone enlighten me as to what's going on? Seems like an additional filter, but i can find no information about it on the web or in the xcms documentation. thanks! matt
