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
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
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
