Dear Li, Your study doesn't seem to present any difficulties for edgeR, and the analysis could be done as a whole. If you would like more detailed advice, you would need to post the targets or samples table from your experiment showing the group membership of each sample, and a description of the questions you want to answer. Best wishes Gordon > From: "Wang, Li" <li.wang at="" ttu.edu=""> > To: Bioconductor mailing list <bioconductor at="" r-project.org=""> > Subject: [BioC] edgeR questions > > Dear List Members > > My experimental design is set to contain two groups of RNA-seq and > within each group there are two subgroups(each subgroup with 8 > replicates). Our goal is to identify differential expression genes > between two groups and also between two subgroups. > I red through the case studies in edgeR user guide and has not found > such cases. > How can we achieve the goals with edgeR? > My current idea is to do the analysis between subgroups first and then > between groups. In the case, we can find the shared and different DE > genes. > I donot know if we can do the analysis in one run. > Any comments and suggestions are very much appreciated. > Thanks in advance! > Best wishes > Li ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}