I am trying to analyze a microarray experiment that was completed on an
Agilent single color array platform.
Using Agi4x44Preprocess, I happily went through the early steps of reading,
normalization, filtration. Ended up on impressive heatmaps etc.

Time to move to limma, now. I've been through limma's userguide
(limma_2.18.0), chapter 7.2 (Affymetrix and other single channel designs)
 and I am trying to make sense of the construction of a design matrix.  I
know my basics matrix multiplications, but I don't understand the sense of
those "-1" in my case of single color arrays. More generally, I had made
some specifications in my targets file, with regards to what each population
was, and I am missing how to feed that info into design and contrast
matrices to operate with limma.
Is there any reading that you could recommend?
Thank you in advance.
Massimo P.

a sketch of a sample "targets" file follows

                     X         FileName Treatment GErep Biorep Culture Array
41745_1_1_5    t0_1Gy1  41745_1_1_5.txt       1Gy     1      1      t0 41745
41844_1_4_6    t0_1Gy2  41844_1_4_6.txt       1Gy     1      2      t0 41844
41744_1_1_7    t0_1Gy3  41744_1_1_7.txt       1Gy     1      3      t0 41744
41742_1_4_8    t0_1Gy4  41742_1_4_8.txt       1Gy     1      4      t0 41742
41745_1_2_13 6moA_1Gy1 41745_1_2_13.txt       1Gy     2      1    6moA 41745
41742_1_3_14 6moA_1Gy2 41742_1_3_14.txt       1Gy     2      2    6moA 41742
41741_1_3_15 6moA_1Gy3 41741_1_3_15.txt       1Gy     2      3    6moA 41741
41844_1_3_16 6moA_1Gy4 41844_1_3_16.txt       1Gy     2      4    6moA 41844
41745_1_3_21 6moC_1Gy1 41745_1_3_21.txt       1Gy     3      1    6moC 41745
41844_1_2_22 6moC_1Gy2 41844_1_2_22.txt       1Gy     3      2    6moC 41844
41744_1_2_23 6moC_1Gy3 41744_1_2_23.txt       1Gy     3      3    6moC 41744
41743_1_3_24 6moC_1Gy4 41743_1_3_24.txt       1Gy     3      4    6moC 41743

-- 
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto

	[[alternative HTML version deleted]]

