[BioC] Limma question

[Naomi Altman]

There is quite a bit of discussion on this list about combining data 
across labs and dealing with other nuisance factors.  There are 
issues in normalization, lab effects, etc.
I think you will learn a lot from reading these  - but you will 
likely not find a complete satisfactory answer.

--Naomi

At 10:34 AM 2/10/2006, alex lam (RI) wrote:
>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.
>
>Thanks,
>
>Alex C. Lam
>PhD student
>Dept. of Genetics and Genomics
>Roslin Institute, Edinburgh
>EH25 9PS
>UK
>
>
>
>-----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.
>
>=--Naomi
>
>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
> >...etc
> >
> >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?
> >
> >Regards,
> >Alex
> >
> >------------------------------------
> >Alex Lam
> >PhD student
> >Department of Genetics and Genomics
> >Roslin Institute (Edinburgh)
> >Roslin
> >Midlothian EH25 9PS
> >
> >Phone +44 131 5274471
> >Web   http://www.roslin.ac.uk
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>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

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