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bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://quantms.org
MIT License
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Enable MBR in DIA-NN step #238

Open daichengxin opened 2 years ago

daichengxin commented 2 years ago

Description of feature

Now, due to make things as parallelisable as possible, Thus, step 2 consists of analysing each run separately with the in silico library generated in step 1. so we should think about adding MBR in one big node . See details: https://github.com/bigbio/quantms/issues/164

calizilla commented 1 year ago

Hi, this is marked as completed, but I don't see the --reanalyse parameter anywhere in the code. What was the strategy to implement MBR for parallelised DiaNN?

ypriverol commented 1 year ago

@calliza you are right. Let me re-open the issue.

michaelsteidel86 commented 11 months ago

Is this still considered as an open issue? To my understanding the re-analysis step based on the empirical library actually is an MBR -analysis. Please correct me if I am wrong. So --re-analysis is only required if full analysis (1st and 2nd pass) are being in one step (non-parallelized)

calizilla commented 10 months ago

Is this still considered as an open issue? To my understanding the re-analysis step based on the empirical library actually is an MBR -analysis. Please correct me if I am wrong. So --re-analysis is only required if full analysis (1st and 2nd pass) are being in one step (non-parallelized)

Yes I think you are correct, apologies for causing a re-open, I was new to DIA-NN at the time.