Closed bpben closed 1 year ago
I think the behavior is probably the same on C++ and python side. e.g., median gets registered here: https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/FILTERING/DATAREDUCTION/MassTraceDetection.cpp#L53-L54 So maybe it is a combination of parameters that is not supported. @cbielow you have been using FFM quite frequently in the past for direct infusion. Do you see some obvious problem here?
so problem is the smoothing?
can you set the smoothing parameter in FFM to false and try if it works? https://github.com/OpenMS/OpenMS/blob/bf46a11720e76a406addbaafdddaff9f6a48515f/src/openms/source/FILTERING/DATAREDUCTION/FeatureFindingMetabo.cpp#L289
to false
I don't think it is the smoothing. I think in general nothing is implemented to get the median quantity of a mass trace. It is the getIntensity function
it is: https://github.com/OpenMS/OpenMS/blob/bf46a11720e76a406addbaafdddaff9f6a48515f/src/openms/source/KERNEL/MassTrace.cpp#L370 but only if not smoothed
Ah thanks. Correct.
Thanks for the quick responses, appreciate this! If I change the use_smoothed_intensities parameter to "false", it works! That seems to solve it, though haven't looked into the smoothing approach - is it the case that taking the median means the smoothing isn't required?
I think the error message means that smoothing doesn't make sense for direct infusion data. I will repurpose this issue to a documentation task.
What is the documentation todo here?
might need domain knowledge. @axelwalter may I assign you here?
Fixed here. The median quantification method will now be used with smoothing enabled and disabled. It was already documented that the median method should be used for direct infusion data.
Hi, I'm using the tutorial example for [untargeted metabolomics[(https://pyopenms.readthedocs.io/en/latest/feature_detection.html?highlight=FeatureFindingMetabo#metabolomics-untargeted). When I use quant_method "median" in the MassTraceDetection step I get an error when running
FeatureFindingMetabo.run
:RuntimeError: this method has not been implemented yet. Feel free to complain about it!
My code is below. If I change quant_method to "area", it works fine. I'm assuming that quant_method "median" hasn't been implemented in the FeatureFindingMetabo algorithms, but I wanted to check. If it hasn't been implemented, is it possible to point me to some way I could make a workaround? I'm not familiar with C++, so not sure if I could implement it.
Just as a note - median is suggested as a method for direct injection, which is the source data I'm using at the moment.