[BioC] limma question

[Fangxin Hong]

> 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



-- 
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