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const-ae / proDA

Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/
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Can proDA be used for paired data? #12

Closed hukai916 closed 2 years ago

hukai916 commented 2 years ago

Hi, quick question, can proDA perform differentially abundant protein analysis on paired samples?

Thanks!

const-ae commented 2 years ago

Hi hukai916,

yes, you would specify the design as.~ subject + condition.

For more background, proDA uses a design matrix to specify what kind of model is fit. This is the same approach that is used for (generalized) linear models including DESeq2. I recommend to take a look at its vignette which goes into great detail explaining how to specify different models including how to analyze paired samples.

Best, Constantin