Question: question about design for limma time course, 2 conditions and drug treatment microarray experiment
5.9 years ago by
Guest User • 12k
Guest User • 12k wrote:
Dear list, 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), levels=design) 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! Best, Ninni -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale:  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 > -- Sent via the guest posting facility at bioconductor.org.
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