[BioC] limma question
Na at uthscsa.edu
Wed Nov 10 17:44:05 CET 2004
I have some questions about the chapter 9 in limma user's guide. Please forgive my lack of statistical knowlege.
1. For the example in section 9.4 technical replication II
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?
2. For the dye swap example in section 9.3 technical replication I
>fit<-lmFit(MA,design, block=c(1,1,2,2), correlation=corfit$consensus)
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?
I couldn't find statistician who specialized in microarray in my area, could you explain it briefly or point me to some direction to study on it? I would appreciate any help.
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