Recently I have been learning limma manual, as a white letter to read the manual completely read mumbo-jumbo, there are many places do not understand, there is no doubts about God, be grateful.
Such is the case ：
fit <- lmFit(eset.rma[present.probes,], design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
What do these lines mean? I know the third step is the Bayes test, but what does Bayes test do? And what's the function of the first two steps?
Finally, there are a few more questions about the Affy package ，I read the manual and felt that the main function of the Affy package was for chip pre processing .For example, restore the original image of the chip ,draw RNA degraded images to see the quality of the chip ,draw the bottom figure to see whether the chip data standardization ,then standardization using RMA methods .Finally, the limma package is used to analyze standardized data .Is my understanding correct, please?