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mildpiggy / DEP2

An r package for proteomics data Analysis, developed from DEP.
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Setting up a paired analysis #8

Open luizalmeida93 opened 6 months ago

luizalmeida93 commented 6 months ago

Hi,

I am unsure how to create an experimental design that takes into consideration paired samples. For example, a group of samples that has measurements in time zero (T0) and then 20 days post treatment (T20).

In other tools, to indicate samples were paired, we have to use the same sample number in the replicate (or bioreplicate) column. However, the examples I saw on the DEP2 website all use repeated numbers, but there is no mention of a paired analysis. Thus, I am wondering how to deal with such a design in DEP2.

I am attaching two examples of how I would proceed for a paired and unpaired analysis if I was using other tools (such as MSstats). Note that paired analysis has a repeated 1-5, while unpaired analysis goes from 1-10. UnpairedAnalysis.csv PairedAnalysis.csv

mildpiggy commented 2 months ago

You can paired analysis though increase the replication in test_diff design_formula: test_diff(se = imputed, type = "manual", test = "T20_vs_T0", design_formula = ~ 0 + condition + replicate)