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MSstats_​statPostProcessing_​iPRG2015

Uses MSstatsConverter to make tables that are processed in short R code scripts in various nodes.
A consensusXML file from an LFQ workflow is required as input.
The outputs are several images and tables accessible through richt clicking the R View and R to Table nodes.

Example input data:
To download the data from the archive linked below, check the box on the folder and click on the download button (arrow) on the top left.
Download and unpack the "Example_Data" data into a directory "Example_data" right inside your KNIME workspace.

URL: Home of the OpenMS plugin https://www.openms.de/
URL: Example Data https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/

Connect and set output path inscript to write all plots to a folder Post-processing LFQ results with MSstatsUses MSstatsConverter to make tables that are processed in short R code scripts invarious nodes.A consensusXML file from an LFQ workflow is required as input.The outputs are several images and tables accessible through richt clicking the RView and R to Table nodes. Calculate groupcomparisonsof interestconsensusXMLto MSstats csvstartKNIME workspaceand load data into MSstatsformatQC plotsRename results(spike-ins havefake IDs)all resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-FNode 24write allplots to a folderconsensusXMLwrite Filefor backupexperimental designinput mzmlsfor mappingFile Reader(deprecated) R to R MSstatsConverter Table to R R View (Workspace) R to R R to Table R to Table R View (Workspace) URI Port toVariable R to Table File Importer File Exporter File Importer File Importer Connect and set output path inscript to write all plots to a folder Post-processing LFQ results with MSstatsUses MSstatsConverter to make tables that are processed in short R code scripts invarious nodes.A consensusXML file from an LFQ workflow is required as input.The outputs are several images and tables accessible through richt clicking the RView and R to Table nodes. Calculate groupcomparisonsof interestconsensusXMLto MSstats csvstartKNIME workspaceand load data into MSstatsformatQC plotsRename results(spike-ins havefake IDs)all resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-FNode 24write allplots to a folderconsensusXMLwrite Filefor backupexperimental designinput mzmlsfor mappingFile Reader(deprecated) R to R MSstatsConverter Table to R R View (Workspace) R to R R to Table R to Table R View (Workspace) URI Port toVariable R to Table File Importer File Exporter File Importer File Importer

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: alka
Created at: 2018-04-16
On NodePit since: 2019-08-04
Last update: 2024-11-23
Created with KNIME version: v5.2.1
Tags: OpenMSMass SpectrometryMSstatsProtein quantification

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