On 12/22/11 4:18 PM, Simon Anders wrote: > Hi > > On 2011-12-22 21:41, Duke wrote: >> I am testing the DEXSeq package with a public RNA-Seq data. >> Unfortunately this data set does not have replicates, only two set of >> data with two conditions. I tried DEXSeq but got error. I checked the >> estimateDispersion function but there is no similar option like in DESeq >> where we can use for non replicate data. Is there any way to overcome >> this disadvantage of the data and finish the DEXseq analysis for it, or >> it is simply a no-go? > > I am starting to regret that we ever offered the "blind" mode with > DESeq. The existence of this feature seemed to have misled too many > users into believing that it is possible to perform a sensible > analysis of RNA-Seq data without replication. It was, however, always > only meant as a tool to salvage what is left from a botched > experiment, and most of the time this will not be much. > > The analysis that DEXSeq attempt has much higher demands on data > quality so that offering such a function would be even less likely to > be of use. > > Nevertheless, it is actually possible to inject manually a dispersion > estimate: simply add a column "dispersion" to the feature data slot > and populate it with some wild guess of what the dispersion might be, > e.g. by writing "fData(ecs)$dispersion <- .1" to set a common > dispersion of 0.1. Then, one can continue with the test even without > replicates. > > Obviously, this is not advisable except for exploratory purposes as > any value one might inject will be nearly impossible to justify. Thanks Simon. I will find another dataset to start with then. Bests, D.