9 Mar 01:46 2014

## edgeR time series analysis question

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@...> > To: bioconductor@..., audra.loy@... > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor