[BioC] Dealing with technical replication with a common reference design

Gordon Smyth smyth at wehi.edu.au
Sat Oct 1 08:55:47 CEST 2005

At 08:43 PM 12/09/2005, michael watson \(IAH-C\) wrote:
>Thanks Gordon
>When I called duplicateCorrelation, I got three warning messages:
>Too much damping - convergence tolerance not achievable in: glmgam.fit(
>etc etc)
>My corfit$consensus was then positive, even though it is a dye-swap
>experiment.  Presumably this means I don't have to treat the technical
>replicates in any special way...?

That would be my interpretation, if everything else is correct. Technical 
variation often dominates biological. If the correlation is much larger 
than zero however, something is wrong.


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