[BioC] DESeq2 dispersion estimate gets stuck

[Carl Herrmann]

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

-- 
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C a r l    H E R R M A N N
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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