[BioC] limma help - choosing an approach

[john seers (IFR)]

Thank you very much for the reply Naomi.

So, am I right in thinking that this is not a usual approach? I have
been told that this is a standard design and that Genespring et al
handle it routinely. Everything I look at in limma is tantalisingly
close to what I want but not quite. I am wondering if I am making it
more difficult than it is?

Can you tell me what you mean by the "factor effects" model? i.e. is it
in the limma userguide? 

Regards


John Seers



 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

tel +44 (0)1603 251497
fax +44 (0)1603 507723
e-mail john.seers at bbsrc.ac.uk                         
e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ 
 
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www.foodandhealthnetwork.com


-----Original Message-----
From: Naomi Altman [mailto:naomi at stat.psu.edu] 
Sent: 12 September 2006 13:16
To: john seers (IFR); bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] limma help - choosing an approach


The only text I know that covers the two-factor factorial design with 
added control is Experimental Design by W. Federer.  It is out of 
print, but should be available in a university library.

In the limma context, I would use separate analysis of 2 channel data 
and use the "factor effects" model that considers each treatment 
combination to be a treatment.  Limma in any case uses contrasts 
rather than computing factor effects, and you probably know which 
treatments you want to compare, so the additional controls should not 
create any problems.

--Naomi

At 04:57 AM 9/12/2006, john seers \(IFR\) wrote:
>
>Hello
>
>I am trying to analyse some slides but I am a bit stumped. The arrays I
>have been given vary with time and a concentration of a substance. i.e
>two experimental dimensions (See targets data below). What is throwing
>me is that the zero concentration is only in the control and I cannot
>work out what model is suitable for this. Can anybody help with some
>advice or tips on the approach to use?
>
>I have looked at the factorial design and the timecourse but neither
>seem to offer a comparison/contrast against the control. Is there a way
>to do this? Do I have to use the "Separate Analysis of Two Channel
data"
>in Chapter 9?
>
>Any advice gratefully appreciated.
>
>Regards
>
>
>John Seers
>
>
>
>
>  My targets file looks like this:
>
>
>
>
>SlideNumber FileName Cy3 Cy5 Time conc
>598 598new.gpr f100t1 Control t1 c100
>599 599new.gpr f20t4 Control t4 c20
>600 600new.gpr f100t4 Control t1 c100
>617 617new.gpr f20t1 Control t1 c20
>621 621new.gpr f20t1 Control t1 c20
>637 637new.gpr f20t4 Control t4 c20
>638 638new.gpr f20t1 Control t1 c20
>639 639new.gpr f100t1 Control t1 c100
>748 748new.gpr f20t4 Control t4 c20
>751 751new.gpr f20t4 Control t4 c20
>833 833new.gpr f100t4 Control t4 c100
>835 835new.gpr f100t1 Control t1 c100
>836 836new.gpr f100t4 Control t4 c100
>957 957new.gpr f100t1 Control t1 c100
>958 958new.gpr f20t1 Control t1 c20
>
>
>
>
>
>
>---
>
>John Seers
>Institute of Food Research
>Norwich Research Park
>Colney
>Norwich
>NR4 7UA
>
>
>tel +44 (0)1603 251497
>fax +44 (0)1603 507723
>e-mail john.seers at bbsrc.ac.uk
>e-disclaimer at http://www.ifr.ac.uk/edisclaimer/
><http://www.ifr.ac.uk/edisclaimer/>
>
>Web sites:
>
>www.ifr.ac.uk <http://www.ifr.ac.uk/>
>www.foodandhealthnetwork.com <http://www.foodandhealthnetwork.com/>
>
>
>         [[alternative HTML version deleted]]
>
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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