[BioC] Replicate quality assessment?

Luckey, John John.Luckey at joslin.harvard.edu
Mon Mar 24 15:49:05 MET 2003

Hello all,
I am looking for a quantitative measure of replicate quality to know if one should be tossed or not. Right now, its a gestalt from pairs and mva plots after running rma on datasets across all replicates and covariates. Would like your experience on reasonable method for quantifying "goodness of replication". 
Idea one: simply to use variance measure displayed in mva.pairs plots (This is function of my statistically ignorant empirical assessment- most replicates seem to fall <0.4 while between covariates is usually >.45).
Alternate method might be use the slope of the fitted line on qq plots (or y intercept) of the M values? Does that measure sound at all reasonable? Is there any real difference between this and variance measurement above?
Towards that end, I have been working with data in S-plus and making qq plots there on M values, is there easy way (ie function) within R to go from exprs values to qq plots of M values (or for that matter- to easily go from exprset object to MVA and QQ plots between covariates?)
Tnaks in advance for your advice,

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