[BioC] Replicate Analysis

[Park, Richard]

Hello everyone, 
I was wondering if anyone knew of a function within bioconductor or method to provide some sort of metric for replicate quality analysis. I have typically been using multipanel graphs (having each replicate plotted vs each other) to get a sense of the replicate qualities. However, I have not been able to find metric that would be good at determining how good a replicate is? 
 
I have tried using various outlier elimination methods to count the number of genes being eliminated for each replicate. I have found this to be reasonable for accounting global differences between the sets, but I think it would be useful for analyzing local areas of differences between replicates. 
 
If anyone has any ideas, I would be most grateful. 
 
Thanks, 
Richard Park 
Computational Data Analyzer
Joslin Diabetes Center 

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