Hey,

As a beginner to the limma package I tried to understand how to define a
design  matrix. I did both experiment examples in the "Limma user's Guide"
manual. Afterwards I wanted to do it with my own data. Here I encounter a
few problems.

As an example I used four Control samples and 4 treated samples.
1. This is how my target files looks like:
filename            treated time.h  conc.
ctrl_1.cel             no    24    0
ctrl_2.cel             no    24    0
ctrl_3.cel             no    24    0
ctrl_4.cel             no    24    0
treat_100_1.cel     yes    24    100
treat_100_2.cel     yes    24    100
treat_1000_3.cel    yes    24    1000
treat_1000_4.cel    yes    24    1000

2. I would like to create a design matrix to compare all 4 wt files with all
4 ctrl files. But I also want to see the differences between the two
concentrations (100, 1000). I have a problem creating the different
coefficients.
How do I choose which coefficient to build?

I would be happy for any help. I didn't find much information about the
limma package and the affymetrix (single-channel) chips. If you can help me
looking for general information I'll be also grateful.


THX,

Assa


--
Assa Yeroslaviz
Loetzener Str. 15
51373 Leverkusen

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