Hi bioC User,

I have a set of 18 Affymetrix arrays with three different conditions. The
annotation looks like that:
number    condition    group
19    wt    total
20    wt    total
21    wt    total
22    LiCl    total
23    LiCl    total
24    LiCl    total
25    wt    low
26    wt    low
27    wt    low
28    LiCl    low
29    LiCl    low
30    LiCl    low
31    wt    high
32    wt    high
33    wt    high
34    LiCl    high
35    LiCl    high
36    LiCl    high

for each of the groups total, low and high I would like to compare wt vs.
LiCl (treatment).
I was trying to create a design matrix for the complete data set, but
somehow I am mixing everything up.

Can someone please help me with the with the correct construction of the
design matrix.

If I understand it correctly it should looks like this:
1    0    0    0    0    0    0
1    0    0    0    0    0    0
1    0    0    0    0    0    0
0    1    0    0    0    0    0
0    1    0    0    0    0    0
0    1    0    0    0    0    0
0    0    1    0    0    0    0
0    0    1    0    0    0    0
0    0    1    0    0    0    0
0    0    0    1    0    0    0
0    0    0    1    0    0    0
0    0    0    1    0    0    0
0    0    0    0    1    0    0
0    0    0    0    1    0    0
0    0    0    0    1    0    0
0    0    0    0    0    1    0
0    0    0    0    0    1    0
0    0    0    0    0    1    0

But somehow I can neither create it nor write the right header.
I would appreciate your help

Thanks
Assa

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