[BioC] DEXSeq without replicates?

[Duke]

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.