[BioC] Addendum: technical replicates (again!): a summary

[Ramon Diaz-Uriarte]

I forgot to add that, under 

> 3. Take the average of the technical replicates
> ****************************************************
> Except for being possibly conservative (and not estimating tech. reps.
> variance component), I think this is a "safe" procedure.
> This is what I have ended up doing routinely after my disappointing tries
> with lme
> (https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-September/002430
>.html) and what Bill Kenworthy seemed to end up doing
> (https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-January/003493.h
>tml).
>
> I think this is also what is done at least some times in literature (e.g.,
> Huber et al., 2002, Bioinformatics, 18, S96--S104 [the vsn paper]).
>
> *********


If we have multiple treatments or conditions, and one single type of control, 
and we hybridize each treatment against the control, then we can analyze 
these experiments, after taking the mean of the tech. reps., following, for 
instance, the example in section 7.2 of the limma mannual ("Affymetrix and 
Other single-channel designs").

I think this set-up is not that rare in some places.


R.