[BioC] DESeq. Error message on estimateDispersions blind

[Simon Anders]

Hi Alex

On 15/07/13 19:33, Alex Koeppel wrote:
> However, when I do estimateDispersions(method="blind") on the same input, I
> get the following error:
>
> "Error in parametricDispersionFit(means, disps) :
>    Parametric dispersion fit failed. Try a local fit and/or a pooled
> estimation. (See '?estimateDispersions')"
>
> I tried using method="pooled", as the message recommends, and that did
> work, but I'm not completely sure if it is ok to use the pooled results for
> my PCA or not.

No, pooled estimation is not appropriate for PCA. You should rather try 
a local fit (fitType="local").

   Simon