**0**wrote:

Dear all,

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 |

gene1 | |||||

gene2 | |||||

gene3 | |||||

gene4 |

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.

Regards.

**36k**• written 8 months ago by zhang.jianhai •

**0**