[BioC] edgeR time series analysis question
Gordon K Smyth
smyth at wehi.EDU.AU
Sun Mar 9 01:46:35 CET 2014
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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