[BioC] question about design for limma time course, 2 conditions and drug treatment microarray experiment
Ninni Nahm [guest]
guest at bioconductor.org
Fri Nov 22 16:03:02 CET 2013
I have a conceptual question about creating a design matrix for a more complicated experimental design.
I have microarray data of
- two different conditions (treatment/control),
- over a series of time points (20, 45, 90, 180 minutes)
- and different dose concentrations of a certain drug (no treatment, 1mg, 2mg, 3mg, 4mg, 5mg).
- and I have 2 replicates per drug, time point, and condition
I think, I know how to do it when I want to consider time only (please correct me when I'm wrong!):
## find genes which change over time differently between the treatment and the control.
cont.dif <- makeContrasts(
Dif1 = (treatment_1mg_tp45-treatment_1mg_tp20)-(control_tp45-control_tp20),
Dif2 = (treatment_1mg_tp90-treatment_1mg_tp45)-(control_tp90-control_tp45),
Dif3 = (treatment_1mg_tp180-treatment_1mg_tp90)-(control_tp180-control_tp90),
However, I would like to know which genes are changing over time and drug exposure between control and treatment.
Would I have to do the contrasts for every dose?
Any help is much appreciated!
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 sva_3.8.0 mgcv_1.7-27 nlme_3.1-113 corpcor_1.6.6 limma_3.18.3
loaded via a namespace (and not attached):
 grid_3.0.2 lattice_0.20-24 Matrix_1.1-0
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