Proteomics DEA

Question

[frarodmar17]

I have proteomics data where most proteins do not follow normal distribution. I am not sure if it would be better to perform a specific differential expression analysis, or if I could log2transform and normalize data (for example, thorugh Quantile method), and after that, performing DEA with limma.

[ATpoint]

limma is a specific differential expression analysis --in my opinion the most generic and useful one for most HT datasets.

[frarodmar17]

But resuts are much worse than Wilcoxon test, because most proteins do not follow normal distribution.

[ATpoint]

limma does not require normal distribution. It is one of the most extensively used testing framework for any OMICS dataset.