Hi, I got an below error message while running the edgeR. > d10 <- estimateTagwiseDisp(d10, prior.n = 10, grid.length = 500) Using grid search to estimate tagwise dispersion. > prior.n10 <- estimateSmoothing(d10) Warning message: In .odls(scores.g = scores, info.g = exp.inf) : Estimate of overdispersion of likelihood scores is strictly zero. Returning min val close to zero (1e-08). I was not sure, what does this mean? Can anyone help me to troubleshoot this? I would great appreciate it. Thanks, Sridhara -- Sridhara G Kunjeti PhD Candidate University of Delaware Department of Plant and Soil Science email- sridhara@udel.edu Ph: 832-566-0011 [[alternative HTML version deleted]]

Dear Sridhara, This is not an error message, it's a just an informative message that your data looks Poisson (dispersion=0) rather than negative binomial (dispersion>0). Please note the help page for estimateSmooth(), which tells you that we do not recommend using this function. I am currently recommending that you set prior.n = 30 / residual.df, where residual.df is the number of libraries subtract the number of groups. This has been made the default value now in the devel version of edgeR. Best wishes Gordon > Date: Fri, 27 May 2011 21:37:10 -0400 > From: Sridhara Gupta Kunjeti <sridhara at="" udel.edu=""> > To: bioconductor at r-project.org, bioconductor-request at r-project.org > Subject: [BioC] error message in edgeR > > Hi, > I got an below error message while running the edgeR. > >> d10 <- estimateTagwiseDisp(d10, prior.n = 10, grid.length = 500) > Using grid search to estimate tagwise dispersion. >> prior.n10 <- estimateSmoothing(d10) > Warning message: > In .odls(scores.g = scores, info.g = exp.inf) : > Estimate of overdispersion of likelihood scores is strictly zero. > Returning min val close to zero (1e-08). > > I was not sure, what does this mean? Can anyone help me to troubleshoot > this? > I would great appreciate it. > > Thanks, > Sridhara > > -- > Sridhara G Kunjeti > PhD Candidate > University of Delaware > Department of Plant and Soil Science > email- sridhara at udel.edu > Ph: 832-566-0011 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}