[BioC] Limma with block and replicate measurement

Yanyan Li yli at mail.jci.tju.edu
Fri Dec 1 17:52:37 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


The documents accompanying this transmission may contain confidential 
health or business information.  This information is intended for the use 
of the individual or entity named above. If you have received this 
information in error, please notify the sender immediately and arrange for 
the return or destruction of these documents.

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

More information about the Bioconductor mailing list