[BioC] Is it possible to fit a hierarchical linear model in LIMMA?

Naomi Altman naomi at stat.psu.edu
Wed Mar 8 02:11:44 CET 2006

I think I am missing something here.   You have written a standard 
linear mixed model which can be handled by any mixed model routine.

The only way you could gain by using limma is if there is also some 
"k" and a linear model for each of the k responses.  (Usually "k" is 
the gene id, but it could be any indicator of a high dimensional response.)

If there is such a "k", I think that you could use the "block" option 
in limma to fit this model.


At 04:47 PM 3/7/2006, pingzhao Hu wrote:
>Say two groups A and B. Each group has 10 individuals.
>Assume that we have two variables: Y and X.
>Therefore, the hierarchical linear model will like:
>Yij=B0i+B1Xij+ERRORij, (i=A,B; j=1,2,...,10)
>We are interested in testing the significance of B1.
>Although some R packages can do this job, we are interested in
>using the shrinkage property in LIMMA or other R packages.
>Thank you for your help in advance!
>Pingzhao Hu
>The Center for Applied Genomics
>The Hospital for Sick Children
>Toronto, Canada
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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