One post has caught my attention (https://support.bioconductor.org/p/35159/), which highlights how to "skip" the eBayes function. First, I understand that Bayes methodology is why limma is so popular and the benefits of utilizing such methods. But if one calculated the t-values and p-values as specified (code below), is there anything that distinguishes the results from ordinary least square if lmFit(method='ls") is used? In other words, if I wanted to compare empirical bayes results to ordinary least square results, would this be an appropriate way to examine the differences?
How to calculate t-value and p-values manually:
fit2$t <- fit2$coef/fit2$stdev.unscaled/fit2$sigma fit2$p.value <- 2 * pt(-abs(fit2$t), df = fit2$df.residual)