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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