[BioC] DE in EdgeR

[R [guest]]

I am testing DE between two groups that each contain 10 time points. 

I am creating my design matrix like this:

Condition <- factor(c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT","WT","WT","WT","WT","WT","WT","WT","WT"))
Condition <- relevel(Condition, ref="WT")
Time <- factor(c("0H","3H","6H","9H","12H","18H","21H","24H","27H","0H","3H","6H","9H","12H","18H","21H","24H","27H"))

design <- model.matrix(~Time+Time:Condition)


How do I proceed if i want to compare the whole group (WT) against the other group (KO) considering the time points as replicates. 



 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=nb_NO.UTF-8       LC_NUMERIC=C               LC_TIME=nb_NO.UTF-8       
 [4] LC_COLLATE=nb_NO.UTF-8     LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=nb_NO.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.2.1   DESeq_1.6.1           locfit_1.5-8          org.Mm.eg.db_2.6.4   
 [5] RSQLite_0.11.2        DBI_0.2-5             AnnotationDbi_1.16.19 Biobase_2.14.0       
 [9] edgeR_2.4.6           limma_3.10.3         

loaded via a namespace (and not attached):
 [1] annotate_1.32.3    genefilter_1.36.0  geneplotter_1.32.1 grid_2.14.1       
 [5] IRanges_1.12.6     lattice_0.20-0     RColorBrewer_1.0-5 survival_2.36-10  
 [9] tools_2.14.1       xtable_1.7-0

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