[BioC] DESeq2 stuck running

[Mingfeng Li]

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
*********************************************