[BioC] Limma with block and replicate measurement

Yanyan Li yli at mail.jci.tju.edu
Fri Dec 1 18:18:42 CET 2006

Hi Bioconductors:

I am doing Random Block Design for single-color arrays, consider the 
following target frame:
FileName   Exp     Trt
1                   1         A
2                   1         B
3                   1         C
4                   1         D
5                   2         A
6                   2         B
7                   2         C
8                   2         D
9                   3         A
10                 3         B
11                 3         C
12                 3         D

Each mRNA has 3 replicates (same y location and different x location), I am 
not a biology person, I hope I could express clearly.

Now I want to compare pairwise groups across the 3 experiments, treat Exp 
as block factor (random) and each mRNA is repeated.

How to incorporate random and repeated effects to lmFit command and also 
Is anyone deal with similar situation or any other suggestions?

I appreciate all your help.

Thanks a lot


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Yanyan Li  phone: 215-503-9876, fax: 215-503-3804
MS. Biostatistician
Division of Biostatistics
Department of Pharmacology and Experimental Therapeutics
Thomas Jefferson University
1015 Chestnut St., Suite M100, Mezzanine Floor
Philadelphia, PA 19107

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