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

Nitin Jain nj7w at virginia.edu
Sat May 22 20:23:58 CEST 2004

Try the Local Pooled error (LPE) test on Bioconductor.


On Sat, 22 May 2004 14:17:19 -0400
  "Luckey, John" <John.Luckey at joslin.harvard.edu> wrote:
>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 
>John Luckey
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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