[BioC] How does limma t-test work?

Jorge Miró jorgma86 at gmail.com
Thu Aug 30 23:33:29 CEST 2012


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 eect 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?

More information about the Bioconductor mailing list