Using edgeR can differentiate difference between Treatment and Control using a negative binomial assumption of the data. However, can edgeR be used to simulate data from the null? -- Thanks, Jim. [[alternative HTML version deleted]]

Dear Jim, No, edgeR does not generate simulated data sets for you. Let me gently point out that this is no unique "null" for RNA-Seq or SNP data. Considerable thought needs to go into what distributional assumptions are appropriate for genomic data. You might start by reading some published papers that compare differential expression methods for RNA-Seq, to see what simulations they chose to do. Some authors make available R code to reproduce their simulations. I have no plans to add a simulation function to the public edgeR package. There are plenty of functions in R that readily simulate data, from any distribution that you like. Anyone undertaking a simulation study is undertaking methodological research in statistical bioinformatics. Anyone qualified to undertake methodological research will have particular requirements for their simulation that are hard to predict in advance, and should be easily able to write simulation code for themselves, or so it seems to me. Best wishes Gordon > Date: Thu, 1 Sep 2011 09:25:23 -0400 > From: Jim Silverton <jim.silverton at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: Re: [BioC] edgeR > > Using edgeR can differentiate difference between Treatment and Control using > a negative binomial assumption of the data. However, can edgeR be used to > simulate data from the null? > -- > Thanks, > Jim. ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}