Hi, How does edgeR handle continuous variables? I would like to include variables like age and BMI in my analysis. As far as I have seen there is no case study in the documentation, please correct me if I am wrong or refer to a place where this is discussed. Especially, glmLRT produces a logFC value also for continuous variables if they are included in the design matrix. How is that calculated and does it make sense to do this? The reason I want to include this is to correct for e.g. age effects on a metagenome sample set. Sincerely, Fredrik Karlsson Systems and Synthetic Biology Department of Chemical and Biological Engineering Chalmers University of Technology Kemivägen 10, SE-412 96 Göteborg, Sweden Office: Room 3057B Tel+46(0)31-772 3886 www.sysbio.se<http: www.sysbio.se=""/> [[alternative HTML version deleted]]

Hi Fredrik, Short answer is yes -- edgeR GLM will handle continuous covariates. Correct, there is no case study on this, but it's just another variable/covariate and I guess categorical variables (designed experiments) are more common. The logFC in this case is the (log of the) multiplicative effect of a single unit increase in the covariate. I googled an example (See Slides 7-9): http://courses.education.illinois.edu/EdPsy589/lectures/4glm3-ha- online.pdf Hope that helps. Best, Mark ---------- Prof. Dr. Mark Robinson Bioinformatics, Institute of Molecular Life Sciences University of Zurich http://tiny.cc/mrobin On 09.01.2013, at 14:47, Fredrik Karlsson wrote: > Hi, > > How does edgeR handle continuous variables? I would like to include variables like age and BMI in my analysis. As far as I have seen there is no case study in the documentation, please correct me if I am wrong or refer to a place where this is discussed. > Especially, glmLRT produces a logFC value also for continuous variables if they are included in the design matrix. How is that calculated and does it make sense to do this? > > The reason I want to include this is to correct for e.g. age effects on a metagenome sample set. > > Sincerely, > > Fredrik Karlsson > > Systems and Synthetic Biology > Department of Chemical and Biological Engineering > Chalmers University of Technology > Kemiv?gen 10, SE-412 96 G?teborg, Sweden > Office: Room 3057B > Tel+46(0)31-772 3886 > www.sysbio.se<http: www.sysbio.se=""/> > > > > [[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