[BioC] number of Replicates - Fold change vs Limma or Siggenes/SAM

Luckey, John John.Luckey at joslin.harvard.edu
Sat May 22 20:17:19 CEST 2004

I am looking to identify differentially expressed genes from five different cell types with five, five, four, four, and three affymetrix replicates each. (I will be using gcrma as preprocessing step)
I seem to remember a paper that showed that T-tests did not predict known spiked-in changes better than simple fold change until one had 8 or more replicates.
Is there data with known spiked in datasets (or a consensus) that limma or sam/siggenes performs better than straight fold change with such low replicate analysis?
John Luckey

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