Question: limma and matrix design for single channel arrays - in search of a primer.
10.4 years ago by
Massimo Pinto • 390
Massimo Pinto • 390 wrote:
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]]
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