[BioC] limma design problem with a two color dataset

[Yong Li]

Dear list,

I am analyzing a two color microarray dataset using limma. The dataset 
is from ArrayExpress database (accession number E-MEXP-1949). The 
samples include 4 mutants (rcd11, rcd13, rcd14 and sro11) and wild-type 
Col0. For the 4 mutants there are 4 biological replicates each. For Col0 
there are also 4 biological replicates but for each biological replicate 
there are 4 technical replicates. The targets I made is as the following:

 > targets
                    FileName      Cy3      Cy5
1         122.rcd1.gpr.proc rcd11.r1  Col0.r1
2          124.354.gpr.proc sro11.r1  Col0.r1
3          125.466.gpr.proc rcd14.r1  Col0.r1
4          126.500.gpr.proc rcd13.r1  Col0.r1
5         133.rcd1.gpr.proc rcd11.r2  Col0.r2
6          134.354.gpr.proc sro11.r2  Col0.r2
7          135.466.gpr.proc rcd14.r2  Col0.r2
8          136.500.gpr.proc rcd13.r2  Col0.r2
9   140.90506.0001.gpr.proc  Col0.r3 rcd11.r3
10 141.090506.0001.gpr.proc  Col0.r3 rcd14.r3
11 142.090506.0001.gpr.proc  Col0.r3 rcd13.r3
12 143.090506.0001.gpr.proc  Col0.r3 sro11.r3
13 152.110506.0001.gpr.proc  Col0.r4 rcd14.r4
14 153.110506.0001.gpr.proc  Col0.r4 rcd13.r4
15 154.110506.0001.gpr.proc  Col0.r4 rcd11.r4
16 155.110506.0001.gpr.proc  Col0.r4 sro11.r4

I am interested in finding DE genes between different mutants (rcd11...) 
and wild-type Col0. Reading in the data and normalization have been done 
but I was not able to make a design matrix. I have read the whole limma 
users guide, especially the part dealing with technical replicates but 
could not find something that is similar to this.

Thanks in advance for your help!

Yong Li