works fine now, thanks


On 12 May 2014 16:03, Michael Love <michaelisaiahlove@gmail.com> wrote:

> Fair enough.
>
> Could you try reinstalling DESeq2? The error is R reporting that this
> function doesn't have an argument which it should have in v1.4.
>
> Mike
>
>
> On Mon, May 12, 2014 at 9:51 AM, Marco Marconi <marco.marconi@gmail.com>
> wrote:
> >
> > mmm....have a look :P
> >
> > > sessionInfo()
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> >  [1] DEXSeq_1.10.3           BiocParallel_0.6.0      DESeq2_1.4.4
> >  [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1             GenomicRanges_1.16.3
> >  [7] GenomeInfoDb_1.0.2      IRanges_1.22.6          Biobase_2.24.0
> > [10] BiocGenerics_0.10.0     BiocInstaller_1.14.2
> >
> > loaded via a namespace (and not attached):
> >  [1] annotate_1.42.0      AnnotationDbi_1.26.0 BatchJobs_1.2
> >  [4] BBmisc_1.6           biomaRt_2.20.0       Biostrings_2.32.0
> >  [7] bitops_1.0-6         brew_1.0-6           codetools_0.2-8
> > [10] DBI_0.2-7            digest_0.6.4         fail_1.2
> > [13] foreach_1.4.2        genefilter_1.46.1    geneplotter_1.42.0
> > [16] grid_3.1.0           hwriter_1.3          iterators_1.0.7
> > [19] lattice_0.20-29      locfit_1.5-9.1       plyr_1.8.1
> > [22] RColorBrewer_1.0-5   RCurl_1.95-4.1       Rsamtools_1.16.0
> > [25] RSQLite_0.11.4       sendmailR_1.1-2      splines_3.1.0
> > [28] statmod_1.4.19       stats4_3.1.0         stringr_0.6.2
> > [31] survival_2.37-7      tools_3.1.0          XML_3.98-1.1
> > [34] xtable_1.7-3         XVector_0.4.0        zlibbioc_1.10.0
> >
> >
> >
> > On 12 May 2014 15:49, Michael Love <michaelisaiahlove@gmail.com> wrote:
> >>
> >> hi Marco,
> >>
> >> Always paste the output of sessionInfo(), as it helps maintainers
> diagnose the problem.
> >>
> >> I would guess you are using a release version of DEXSeq, but DESeq2
> version < 1.4?
> >>
> >> Mike
> >>
> >>
> >> On Mon, May 12, 2014 at 9:35 AM, Marco Marconi <marco.marconi@gmail.com>
> wrote:
> >>>
> >>> Hello, i get this strange error:
> >>>
> >>> dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design=
> ~
> >>> sample + exon + condition:exon,flattenedfile=flattenedFile )
> >>>
> >>> Error in DESeqDataSet(se, design, ignoreRank = TRUE) :
> >>>   unused argument (ignoreRank = TRUE)
> >>>
> >>>
> >>> it seems to be an internal error of the DEXSeqDataSetFromHTSeq
> function, I
> >>> couldn't find any workaround....
> >>>
> >>> thanks
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
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> >>
> >>
> >
>

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