[BioC] edgeR time series analysis question

[Gordon K Smyth]

Dear Audra,

I am assuming that you are following Section 3.2.6 (An ANOVA like test for 
any differences) of the edgeR User's Guide, and that you have used

   lrt <- glmLRT(fit, coef=2:6)

If so, then the test is for all possible differences between the 6 time 
points.

The fact that the coefficients are fitted with time 0 as the reference 
level makes no difference.  The test would be identical if another test of 
5 contrasts was used.

Best wishes
Gordon

> Date: Fri,  7 Mar 2014 19:39:49 -0800 (PST)
> From: "Audra Andrew [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, audra.loy at mavs.uta.edu
> Subject: [BioC] edgeR time series analysis question
>
>
> 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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