[BioC] DESeq2 stuck running

Michael Love michaelisaiahlove at gmail.com
Thu May 15 20:17:34 CEST 2014


Just for users who end up on this thread through search: updating to
DESeq2 v1.4.5 clears up this hang.

Mike

On Mon, May 12, 2014 at 1:11 PM,  <lmf.bill at gmail.com> wrote:
> Hi Mike,
> I missed that email. Thank you very much.
>
> Best,
> Mingfeng
>
> Sent from my iPod
>
> On May 12, 2014, at 12:34 PM, Michael Love <michaelisaiahlove at gmail.com>
> wrote:
>
> hi Mingfeng,
>
> I sent a follow-up email that I forgot to bump the version number, and the
> fix will be in 1.4.5, which should be out today.
>
> Mike
>
>
> On Mon, May 12, 2014 at 12:03 PM, Mingfeng Li <mingfeng.li at yale.edu> wrote:
>>
>> Hi Mike,
>>
>> Thanks your help. Unfortunately, it does not work in my computer.  It is
>> still hanged when typing "system.time({nbinomWaldTest(ddsMF)})". I pasted
>> the sessionInfo. Thanks.
>>
>> best,
>> Mingfeng
>>
>>
>> > sessionInfo()
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] DESeq2_1.4.4            RcppArmadillo_0.4.300.0 Rcpp_0.11.1
>> [4] GenomicRanges_1.16.3    GenomeInfoDb_1.0.2      IRanges_1.22.6
>> [7] 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_1.46.1
>> [10] geneplotter_1.42.0   grid_3.1.0           lattice_0.20-29
>> [13] locfit_1.5-9.1       splines_3.1.0        stats4_3.1.0
>> [16] survival_2.37-7      xtable_1.7-3
>>
>>
>>
>> On Sat, May 10, 2014 at 10:43 AM, Michael Love
>> <michaelisaiahlove at gmail.com> wrote:
>>>
>>> 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
>>> > *********************************************
>>
>>
>>
>>
>> --
>> *********************************************
>> 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
>> *********************************************
>
>



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