[BioC] Limma question

alex lam (RI) alex.lam at bbsrc.ac.uk
Fri Feb 10 16:34:11 CET 2006

Dear Naomi,
They are 2-channel arrays but there are many samples. 115 arrays, in fact. I just didn't paste in the whole matrix. And the treatment is actually a SNP genotype, hence 3 treatments. I problem is that there are other factors - line and lab that I want to account for as background nuisance effect, but I don't want to compare 1 genotype from 1 lab with another genotype from another lab. I am interested in comparing the three treatment group.


Alex C. Lam
PhD student
Dept. of Genetics and Genomics
Roslin Institute, Edinburgh
EH25 9PS

-----Original Message-----
From: Naomi Altman [mailto:naomi at stat.psu.edu]
Sent: Fri 2/10/2006 3:05 PM
To: alex lam (RI); bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Limma question
Are these 2-channel arrays?  With 1 sample per treatment you cannot 
do statistical testing, even without the nuisance factors.


At 09:43 AM 2/10/2006, alex lam (RI) wrote:

>Dear colleagues,
>Hi, I would like to ask a question related to creating design matrix in
>limma. Statistics is not my strong subject so I apologise in advance if
>this is a silly question. I have a number of arrays with 3 different
>treatments and I can generate a design matrix using modelMatrix.
> > modelMatrix(targets, ref="Pool")
>Found unique target names:
>  one Pool three two
>        one three two
>samp01   1     0   0
>samp02   0     0   1
>samp03   1     0   0
>But there are other nuisance factors, for example the arrays were
>hybridised in 3 different labs, and the animals are not all from the
>same line. I am only interested in comparing the treatment effect but in
>the analysis I would like to account for the nuisance factors. I have
>been reading the limma user guide and I guess this is a not really
>factorial design, correct? Any idea on how to make this matrix?
>Alex Lam
>PhD student
>Department of Genetics and Genomics
>Roslin Institute (Edinburgh)
>Midlothian EH25 9PS
>Phone +44 131 5274471
>Web   http://www.roslin.ac.uk
>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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