I've GWAS data which are used in tandem with GTEx or in-house database constructed using predixcan software. I was wondering if eBayes can be used with the output from predixcan? The gene-expression values from predixcan are negative and positive, they are inverse normalized.

Predixcan also provides utility to conduct differential gene expression analysis. I'm exploring further as data at hand consist related individuals.

limma can be used with any reasonably normalized log-expression values. I am not familiar with predixcan software or inverse normalization so cannot answer questions about them.