[BioC] DESeq2 dispersion estimate gets stuck

Michael Love michaelisaiahlove at gmail.com
Sat May 10 14:19:19 CEST 2014


hi Carl,

Thanks for reporting this. I had one user report such a hang for
version 1.2, and had implemented a fix for this in version 1.4, so I'm
not sure about this one. I could look into this if you could email me
off list a small example. Is it possible to find a small subset of
rows which produce the hang?

ddssub <- dds[1:100,]
ddssub <- estimateDispersions(ddssub)

And then to remove any identifying information,

colData(ddssub) <- colData(ddssub)[, c("patient","proliferation") ]
levels(ddssub$patient) <- letters[ 1:nlevels(ddssub$patient) ]

Mike

On Fri, May 9, 2014 at 7:51 AM, Carl Herrmann
<c.herrmann at dkfz-heidelberg.de> wrote:
> Hi,
>
> I am analysing a patient dataset for diff. expression with DESeq2 (v
> 1.2.10).
>
> We have several patients, and for each patient we have several samples.
> I am running this analysis on different combinations of samples.
>
> My design has two factors : patient (multilevel) and a second factor
> (proliferation, true/false)
> so : design ~ patient + proliferation
>
> I am interested in diff. expression depending on the proliferation only
> (second factor).
>
> On some combinations, the gene dispersion estimation step
> (estimateDispersion) gets stuck at the gene-wise dispersion estimate.
> I let it run for several hours, and eventually killed the job.
>
> When reducing the number of iterations to 10, it gets stuck. Same problem
> with version DESeq2 v 1.4.0
>
> Strangely, this happens when including samples that, when included in other
> combinations, run just fine.
> So this does not seem to be a problem of the dataset itself.
>
> I am not sure whether this is enough to get a hint on where the problem
> might come from, so please tell me whether I should provide additional
> information.
>
>  Thanks for your help !
>
> Carl
>
> --
> ------------------------------------------------------------------
> C a r l    H E R R M A N N
> ------------------------------------------------------------------
> Institut für Pharmazie und Molekulare Biotechnologie
> Universität Heidelberg
> DKFZ Heidelberg - Department of Theoretical Bioinformatics
> Im Neuenheimer Feld 580
> D-69120 Heidelberg
> tel.: +49 (0) 6221 42-3612
> email : c.herrmann at dkfz.de
> web: http://biologie.univ-mrs.fr/carlherrmann
>
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