SV: [BioC] random block effect and technical replicates within array at the same in linear model using Limma?

[Jakob Hedegaard]

Dear Gordon & list

Why is it not possible to fit random block effect and technical replicates within array in the same linear model?
Is it because
- the statistical theory is not ready? - or
- it is not implemented in Limma?

I am not a statistician so it might be a stupid question :-)

Thanks
Jakob

-------------------------------------------------------------------
Jakob Hedegaard
Danish Institute of Agricultural Sciences
Department of Genetics and Biotechnology
Molecular Genetics and System Biology
Building K25
Research Centre Foulum
P.O. box 50
DK-8830 Tjele
Denmark
Tel: (+45)89991363
Fax: (+45)89991300
-----Oprindelig meddelelse-----
Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af Gordon K Smyth
Sendt: Thursday, June 02, 2005 12:43 PM
Til: Peter Sørensen (HAG)
Cc: bioconductor at stat.math.ethz.ch
Emne: [BioC] random block effect and technical replicates within array at the same in linear model using Limma?

> Date: Thu, 2 Jun 2005 11:47:15 +0200
> From: Peter S?rensen (HAG) <Peter.Sorensen2 at agrsci.dk>
> Subject: [BioC] random block effect and technical replicates within
> 	array at	the same in linear model using Limma ?
> To: <bioconductor at stat.math.ethz.ch>
>
> Dear list,
>
> I have an experiment with 24 arrays.
> I have 3 factors each with 2 levels and 12 blocks (1,1,2,2,3,3,....,12,12).
> Each gene is replicated 4 times on each array.
>
> I know how to fit blocks as random as explained in the Limma manual (Technical replication I)
> I know how to account for the replication within arrays.
>
>
> Is it possible to fit random block effect and technical replicates within array at the same in
> linear model using Limma ?

No it isn't.  (Being able to do so awaits the development of new theory.) See
?duplicateCorrelation 2nd paragraph of "Details:", or ?lmFit 4th paragraph of "Details:".

Gordon

> Thanks
> Peter

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