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@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.
>

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