Dear all, Have you already known about a RNA-seq R Package for the differential expression analysis between multiple samples (ANOVA-like) ? Tools such as edgeR or DESeq seems to be limited to the analysis between two conditions only. thanks Bruno -- Bruno Zeitouni, PhD Institut Curie - U900 INSERM - Mines ParisTech Equipe Bioinformatique Bâtiment de Biologie du Développement 26 rue d'ULM 75248 Paris Cedex 05 - FRANCE Tél : +33 1 56 24 69 31 Mail : bruno.zeitouni@curie.fr [[alternative HTML version deleted]]

Hi Bruno > Have you already known about a RNA-seq R Package for the differential > expression analysis between multiple samples (ANOVA-like) ? > Tools such as edgeR or DESeq seems to be limited to the analysis between > two conditions only. No, they aren't. Both DESeq and edgeR offer ANODEV, i.e. ANOVA with GLMs. For DESeq, we've added the description of this to the vignette only recently (see the devl version) although the functions are available since a while. The edgeR folks describe in their manual, too. Simon

Hi Bruno EdgeR has had GLM methods for many months now. These can be used to perform ANOVA-like analyses (analysis of deviance in GLMs) and can handle any experimental design that can be written as a linear model. The edgeR Users Manual has a worked example of an analysis of a paired design, which is a good place to start. Cheers Davis > Dear all, > > Have you already known about a RNA-seq R Package for the differential > expression analysis between multiple samples (ANOVA-like) ? > Tools such as edgeR or DESeq seems to be limited to the analysis between > two conditions only. > > thanks > > Bruno > > -- > > Bruno Zeitouni, PhD > Institut Curie - U900 INSERM - Mines ParisTech > Equipe Bioinformatique > B?timent de Biologie du D?veloppement > 26 rue d'ULM > 75248 Paris Cedex 05 - FRANCE > > T?l : +33 1 56 24 69 31 > Mail : bruno.zeitouni at curie.fr > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------- Davis J McCarthy Research Technician Bioinformatics Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, Vic 3052, Australia. dmccarthy at wehi.edu.au http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}