Hi all, I'm using limma to analyze a proteomics dataset, basically following the approach described here, so log2(count+1), quantile normalization, then a limma pipeline with eBayes(trend=TRUE, robust=TRUE). However, I was wondering if it is possible to use
vooma on the data somehow, and/or include some precision weights or covariates based on peptide counts and sequence coverage. The peptide count ranges betwen 1 - 185 and the sequence coverage is betwen 0.2 - 90. I trust low peptide count and low sequence coverage less, and would like to use this information during model fitting.