msqrob2 outputs (Protein IDs?)
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@d5ae5ac6
Last seen 19 months ago
United Kingdom

Newbie question, I am wanting to get a sample report output from my msqrob2 analysis, one which has protein IDs and raw abundances for example. Are there any tutorials describing what code to use to enable such a report?

The DE tutorial on msqrob2 is great, but it does not go into enough detail, is there anywhere else that one can get tutorials for using this analysis approach?

msqrob2 • 529 views
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@laurent-gatto-5645
Last seen 10 weeks ago
Belgium

If you use msqrob2, you data is probably stored as a QFeatures object. Assuming it is called qf and the assay with the protein data you want is called "prot", you can get the quantitative data with assay(qf[["prot"]]). You can then write it to a csv file with write.csv(assay(qf[["prot"]]), file = "prots.csv").

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