[BioC] Explaining limma, design matrices and linear models to non statisticians

Natalie P. Thorne npt22 at cam.ac.uk
Mon Feb 27 16:31:20 CET 2006


I have some slides on how to make design matrices that I use to teach 
biologists.  Actually I've been thinking, for a while,  about posting them 
somewhere on Bioconductor for general resource.

I have several slides for two-colour data and a couple for single-color 
data.  The two-color examples, start with very basic experimental designs, 
two samples only, through to 3 samples (direct and ref designs), 4 samples 
factorial design and 2x3 factorial/time series designs.
The slides work through how to select the parameters, including 
alternative parameterisations, how to interpret them, and how to specify 
them in a design matrix.  Its very hands on - I usually get people to work 
through each example by hand so they really get to understand the idea of 
matrix multiplication of the design matrix with the parameter vector and 
how it actually relates to what is measured on each slide.
I've used these over a dozen times for various courses and I find they 
work quite well...of course I usually modify and add slightly to them each 
time.  You are welcome to try them if you like.


BTW: I also have 4 practicals that I use to teach the fundamentals of 
limma (they include RBasics, LimmaBasics, LimmaPreprocessing, 
LimmaDiffExpression).  These have a lot more detail for real beginners 
to R who are trying to use Limma.  The examples are complementary to 
the LimmaUsers guide, but they include more detail on the basics that 
biologists often find hard when they're getting started. The problem is, 
the latter three pracs come with data sets that will probably exceed the 
space limit acceptable by BioConductor.  Also I have the beginnings of a 
Limma "Reference Card".  I guess, I should figure out a sensible way/place 
to post all this.

On Mon, 27 Feb 2006, michael watson (IAH-C) wrote:
> Hi
> I'm going to be teaching use of limma to a bunch of non-statisticians
> later this month, and I wondered if there were any slides or other
> resources that I could possibly hi-jack to explain how and why we create
> design matrices?
> Many thanks
> Mick

Natalie Thorne, PhD
Research Associate
Computational Biology Group
Hutchison/MRC Research Centre
Department of Oncology
University of Cambridge
Hills Rd, Cambridge CB2 2XZ

Email: npt22 at cam.ac.uk
Phone: +44 (0)1223 763381
Fax  : +44 (0)1223 763262

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