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Jorge Miró ▴ 130@jorge-miro-5469
Last seen 7.1 years ago
Hi, I am using the limma package for an analysis of differential expression and have a question about how the t-test in limma works. To my understanding a difference between the usuall t-test and the one used in limma is that the standard error in limma is calculated by using a linear method based on a Bayesian model (I don't really get how it works ). In the users guide of limma it says that "This has the same interpretation as an ordinary t-statistic except that the standard errors have been moderated across genes, i.e., shrunk towards a common value, using a simple Bayesian model. This has the e ect of borrowing information from the ensemble of genes to aid with inference about each individual gene". What exactly does it mean to borrow information from other genes? Is it for example the standard error of a gene on different arrays than the ones been compared or the standard error of all other genes in the same arrays being compared that is being used in the calculations?