[BioC] edgeR time series analysis question

[Audra Andrew [guest]]

Hi,

I have RNAseq data in replicates for 6 time points (0h, 6h, 12h, 24h, 96h, and 10 days).  I want to do time course analysis of this data using GLM. Experimenting, I used a model matrix with an intercept term and the section on the ANOVA-like test for any differences.  My question: Is the list of genes output based on contrasts between all the time points or just between each with the intercept(0h)?  I hope this makes sense. Thanks so much!

Best,
Audra

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tcltk     parallel  stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
[1] maSigPro_1.34.0    DynDoc_1.40.0      widgetTools_1.40.0
[4] MASS_7.3-29        Biobase_2.22.0     BiocGenerics_0.8.0
[7] edgeR_3.4.2        limma_3.18.9      

loaded via a namespace (and not attached):
[1] Mfuzz_2.20.0     tkWidgets_1.40.0 tools_3.0.2 

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