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

[Natalie P. Thorne]

Due to many requests, I will put my resources on a temporary web site for 
anyone who is interested to download.  I should have it up by tomorrow and 
will send the link then.

Natalie


On Mon, 27 Feb 2006, Natalie P. Thorne wrote:

>
> Mick,
>
> 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.
>
> Natalie
>
>
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>

-- 
______________________________
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