[BioC] DEXSeq without replicates?

[Simon Anders]

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.

   Simon