[BioC] DESeq2 stuck running

[Michael Love]

hi Mingfeng,

Thanks for reporting this and sending the example. I found the bug
that produced this hang, and just pushed v1.4.4 (available in 1 day on
Bioc), which fixes this:

> library(DESeq2)
> load("~/Downloads/tmpFile.Rdata")
> system.time({nbinomWaldTest(ddsMF)})
   user  system elapsed
 14.841   0.777  15.634

# or the whole pipeline:

> system.time({DESeq(ddsMF)})
using pre-existing normalization factors
estimating dispersions
you had estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
   user  system elapsed
 38.768   1.457  40.240

Mike


On Fri, May 9, 2014 at 5:38 PM, Mingfeng Li <mingfeng.li at yale.edu> wrote:
> Hi Mike,
>
> Thanks your so fast response. I would like to send you one example in Rdata.
> You can get the information of the design, the normalization factor matrix.
> please reproduce the following codes:
>  library("DESeq2")
> load("tmpFile.Rdata")
> ddsMF = nbinomWaldTest(ddsMF);
>
>
> Best,
> Mingfeng
>
>
>
>
> On Fri, May 9, 2014 at 4:12 PM, Michael Love <michaelisaiahlove at gmail.com>
> wrote:
>>
>> hi Mingfeng,
>>
>> With 6 samples, this is typically seconds to run. If it's taking longer
>> than a few minutes, usually this means something is wrong. Could you make a
>> small reproducible example and send me data and a script? If this is not
>> possible, I'd need some more information, like the code you are using, the
>> design, the normalization factor matrix, etc.
>>
>> Mike
>>
>>
>> On Fri, May 9, 2014 at 3:14 PM, Mingfeng [guest] <guest at bioconductor.org>
>> wrote:
>>>
>>>
>>> It is the exciting news of the coming of DESeq2.
>>> There are many updates and incorporation with other software, e.g., Wald
>>> test and cqn.
>>> My question is the nbinomWaldTest may stuck running for long time when
>>> using multiple factors, e.g., running several days but no results or
>>> messages coming out. It works well when I remove the "type" factor.
>>> I paste the meta data in the following:
>>>            condition type
>>> S103         W  U
>>> S149         W Y
>>> S114         W Y
>>> S98          K  U
>>> S92          K  U
>>> S159         K Y
>>>
>>>
>>>
>>>
>>>
>>>
>>> Thanks.
>>>
>>>
>>>
>>>
>>>  -- output of sessionInfo():
>>>
>>> > sessionInfo()
>>> R version 3.1.0 (2014-04-10)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] splines   parallel  stats     graphics  grDevices utils     datasets
>>> [8] methods   base
>>>
>>> other attached packages:
>>>  [1] cqn_1.10.0              quantreg_5.05           SparseM_1.03
>>>  [4] preprocessCore_1.26.0   nor1mix_1.1-4           mclust_4.3
>>>  [7] DESeq2_1.4.1            RcppArmadillo_0.4.300.0 Rcpp_0.11.1
>>> [10] GenomicRanges_1.16.2    GenomeInfoDb_1.0.2      IRanges_1.22.4
>>> [13] BiocGenerics_0.10.0
>>>
>>> loaded via a namespace (and not attached):
>>>  [1] AnnotationDbi_1.26.0 Biobase_2.24.0       DBI_0.2-7
>>>  [4] RColorBrewer_1.0-5   RSQLite_0.11.4       XML_3.98-1.1
>>>  [7] XVector_0.4.0        annotate_1.42.0      genefilter_1.46.0
>>> [10] geneplotter_1.42.0   grid_3.1.0           lattice_0.20-29
>>> [13] locfit_1.5-9.1       stats4_3.1.0         survival_2.37-7
>>> [16] xtable_1.7-3
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>
>>
>
>
>
> --
> *********************************************
> Mingfeng Li, Ph.D.
> Postdoctoral Associate
> Department  of Neurobiology
> Yale University School of Medicine
> 333 Cedar Street, SHM C-327C
> New Haven, CT 06510
>
> E-mail: mingfeng.li at yale.edu
> Lab: (203) 785-5941
> Lab website: www.sestanlab.org
> *********************************************