MapAlignerPoseClustering and FeatureLinkerUnlabeledQT errors

Thank you very much for all your help! In the meantime, I will wait for the stable version next week and keep trying with different parameters and see if I can get similar results with the nightly version and knime 4.1.1.

Hi,

I think I found the error.
It seems like on of the tools in one of the branches (ID vs quant), uses a different rounding cutoff by now.
If you add two Round Double nodes in front of the Joiner and apply it with decimals = 10
to the cols that you join over (rt and mz), then it works as expected.

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Hi!
Yes! You are perfectly right! Now I get the expected results! Thank you incredibly much!!
It seems though that the order you will insert the files in the “input files” node also plays a role. With the order:
2012_02_03_PStd_050_1.mzML,
2012_02_03_PStd_050_2.mzML,
2012_02_03_PStd_050_3.mzML,
2012_02_03_PStd_10_1.mzML,
2012_02_03_PStd_10_2.mzML,
2012_02_03_PStd_10_3.mzML
you get expected results (23 compounds in the Joiner “Reannotate Original Intensities”). But if you put them differently (let’s say first the 10 and then the 50) the results change.
It is a bit strange because I would guess no matter the order the results should be the same.

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Hi,

the fold change cutoff in one of the R snippets looks for over-expression (>=2 FC).
Therefore I think the order has to be from low concentration to high concentration.

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ach! yes! Now I see! It makes sense! jpfeuffer thank you very much for all your help and time! It was extremely valuable and definitely time-saving! I am looking forward for the next official OpenMS release next week!

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