Dear list, I have an RNA seq experiment data and I intend to extract differentially expressed genes for my data. The data is from two groups(male and female) and I want to know which genes are DE between this two groups. Which approach of edgeR should I use? The classic one with exactTest function or the GLM approach. Thank you for your reply -- output of sessionInfo(): Thank you for your reply -- Sent via the guest posting facility at bioconductor.org.

Dear Sara, Well, the exactTest is applicable in this case, so it would be logical to use it. But both the classic exactTest and the more general glm approaches will give similar results. You don't mention having read any documentation but I presume that you must have read the edgeR User's Guide. The first three case studies in the User's Guide are two group comparisons, and they all use the exactTest. Best wishes Gordon > Date: Tue, 6 Nov 2012 05:47:20 -0800 (PST) > From: "sara [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, swilsonn86 at gmail.com > Subject: [BioC] What is difference between classic and GLM edgeR > > > Dear list, > I have an RNA seq experiment data and I intend to extract differentially > expressed genes for my data. The data is from two groups(male and > female) and I want to know which genes are DE between this two groups. > Which approach of edgeR should I use? The classic one with exactTest > function or the GLM approach. > Thank you for your reply > > -- output of sessionInfo(): > > Thank you for your reply > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}