[BioC] technical replicates and spots in limma

[Ron Ophir]

>
>
>>>> "Gordon K Smyth" <smyth at wehi.EDU.AU> 04/18/05 2:24 PM >>>
>> Date: Sun, 17 Apr 2005 17:24:14 +0300
>> From: "Ron Ophir" <ron.ophir at weizmann.ac.il>
>> Subject: [BioC] technical replicates and spots in limma
>> To: <bioconductor at stat.math.ethz.ch>
>>
>> Dear limma experts,
>> I have direct experiments with two biological replicates and two
>> technical replicates. In each array sots are printted in 4
replicates.
>> In duplicateCorrelation help it is written that "At this time it is
not
>> possible to estimate correlations between duplicate spots and
between
>> technical replicates simultaneously."
>> The question is it possible to average on both technical and spot
>> replicates but not simultaneously and if yes then how?
>> If not which least-squares analysis should I drop technical sample
>> replicates or spots replicates?
>
>The between spot correlation is usually in the range 0.5-0.9. 
Correlations between technical
>replicates are usually not so strong, seldom higher than around
0.2-0.3 and often less.

>
>If you're going to ignore one of these correlations, it should be the
technical replication.  If
>you're going to average over one of the replicate structures, it
should be over the replicate
>spots.

Thanks. Averaging over spot replicates using duplicateCorrelation()
assuming equal space between replicates coordinates or I can give a
vector of spots location like in block for technical replicates.
If the latter is not possible, does the following commands are what
should be done:
spotRep<-as.factor(c(1,1,2,2,3,1,1,3,3,2,2,3,...))
vvRaw$R<-unlist(by(vvRaw$R,spotRep,mean))
vvRaw$G<-unlist(by(vvRaw$G,spotRep,mean))
vvRaw$Rb<-unlist(by(vvRaw$Rb,spotRep,mean))
vvRaw$Gb<-unlist(by(vvRaw$Gb,spotRep,mean))

Ron

>
>The measurement error is often larger than the biological variation,
so that treating the
>technical replicates as biological replicates is often not as bad as
it sounds.  This is what I
>would usually do, having checked the between technical rep correlation
is not large.
>
>Gordon
>
>> Thanks in advance
>> Ron