I am confused about how t-test or F-test is implemented in limma/edgeR.
Let's say I have a small dataset: two conditions, each condition has 3 replicates, and there are 4 genes.
|Con1 rep1||Con1 rep2||Con1 rep3||Con2 rep1||Con2 rep2||Con2 rep3|
My questions is if I use limma/edgeR to analyze the DEGs across the two conditions, does limma first use the regular t-test to calculate if the mean of con1 is significantly different from the mean of con2 for each gene independently? And gets a regular t-statistic? Then use eBayes to adjust the regular t statistic and get the moderated t?
Look forward to your reply.