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

[Nitin Jain]

Try the Local Pooled error (LPE) test on Bioconductor.
Reference:
http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/research/LPE.pdf

-Nitin

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 
>analysis?
> 
>Sincerely,
>John Luckey
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>