[BioC] limma question

Fangxin Hong fhong at salk.edu
Wed Nov 10 20:01:26 CET 2004

> This technique includes an effect for each biological replicate. How about
> technical replicates, does it treat technical replicates as biological
> replicates? Am I right that this technique doesn't consider effect for
> technical replicate?
Biological replicates may have systematic difference (e.g. different
individuals), but technical replicates are purely replicates ( 2 samples
from the same individual) which we generally don't think they have effect
beside error.

> This technique handles technical replicates by using the function
> duplicateCorrelation. Am I right it includes an effect for each technical
> replicates, but not an effect for each biological replicate? how is
> biological replicate's effect handled here?
No, actually this include an (random) effect for each biological
replicate, no effect for technical replicates. block=c(1,1,2,2) means each
each biological replicate form one block.

Hopefully this will help.


Fangxin Hong, Ph.D.
Bioinformatics Specialist
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu

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