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MapRTTransformer does not change RT according to trafoXML #276
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Unfortunately, the @timosachsenberg bug in OpenMS? |
Doesn't the Transformer fit a curve to the found points? If that is the case, it is to be expected that the regression does not necessarily go through all points. |
Yes, I am pretty sure the points are just anchors. The real transformation happens through intercept and slope in the beginning of the file. |
Ah that makes sense! Indeed if I use slope and intercept with the A quick follow-up question: Would you recommend b_spline transformation over linear transformation?
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Not necessarily. A lot of MS programs these days just use a linear transformation AFAIK and it turns out OK. On the other hand, splines wont be a bottleneck in runtime and might yield more overlaps (hopefully without overfitting). I don't think there is a lot that can go wrong with the algorithm itself so the warning might be overly cautious. Especially if you evaluate the results carefully. |
Alright! That is very good to know. Thanks again 🙏🏼 |
Description of the bug
In the map_alignment step the MapAlignerIdentification computes a trafoXML for each respective run/replicate based on a set of replicate idXMLs. However, the MapRTTransformer inserts values not corresponding to the actual information in the trafoXML. If I only pick one idXML from Comet and do MapAlignerIdentification -> MapRTTransformer I get the following:
Example for a peptide AAAAAAQSVY that is only found once in a run:
Before MapAligner: (from idXML)
After MapAligner (trafoXML):
<Pair from="2015.8" to="2029.05" note="AAAAAAQSVY"/>
After MapRTTransformer:
Example with a peptide ATYPYQVVR found 3 times in a replicate:
Before MapAligner: (from idXML)
After MapAligner (trafoXML):
<Pair from="2479.4" to="2487.925" note="ATYPYQVVR"/>
After MapRTTransformer:
There seems to be something wrong with mapping the transformed RTs from the trafoXML to idXML. Needs to be investigated further in the respective OpenMS implementation
Edit: Transforming RT of an mzml has the same issue
Command used and terminal output
nextflow run nf-core/mhcquant -r dev -profile test_full,docker --outdir test_quant
Relevant files
test_quant_issue.zip
System information
No response
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