[BioC] Explaining limma, design matrices and linear models to non statisticians
Natalie P. Thorne
npt22 at cam.ac.uk
Wed Mar 1 20:35:00 CET 2006
As promised, I have put the ppt slides I have for explaining design
matrices on the web for download.
I have also put my limmapracticals (as a zip) on the same site.
Sorry for the delay,
On Mon, 27 Feb 2006, Natalie P. Thorne wrote:
> 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:
>> 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
> 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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
Natalie Thorne, PhD
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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