[BioC] Using edgeR with no replicates, estimating dispersion and the pseudo.alt slot

Mark Robinson mark.robinson at imls.uzh.ch
Fri Oct 26 15:27:11 CEST 2012

Hi Mick,

> useful measures of normalised expression

Would the cpm() function suit your needs?  It's not identical to $pseudo.alt, but should be similar.

Best, Mark

On 25.10.2012, at 17:37, WATSON Mick wrote:

> Hi
> We have a collaborator with RNA-Seq data with no replicates - and yes, I understand the limitations of this.
> In the egdeR manual, one solution suggested to estimating common dispersion is choosing a value based on experience e.g. "d$common.dispersion <- 0.4".  However, this has the disadvantage of not filling up the pseudo.alt slot of the object, which are useful measures of normalised expression.  The estimateTagWiseDisp() function then fails.
> It's fairly trivial to edit the estimateCommonDisp() function to accept a user provided common dispersion value, but I am not sure this is entirely valid.
> The question being how to populate the pseudo.alt slot when you are estimating the common dispersion parameter yourself, and whether it is even valid to do so.
> Cheers
> Mick
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