Combining t and P value adjustment with TREAT

[ndeimler99]

Hello, I have a DIA dataset I am working with. I am interested in using the "treat" method (limma-voom and edgeR offer functions to do so) to determine if the logFC of a protein is significantly higher than that of a biologically meaningful value such as 0.5 instead of comparing it to 0. It is my understanding DEqMS simply adjusts the t and p-statistics reported by eBayes() based on the number of precursors used to identify and quantify each protein. I was wondering if there would be a way to combine these two methodologies.

Thanks,

Nathaniel Deimler