[BioC] DEXseq ignoreRank
Michael Love
michaelisaiahlove at gmail.com
Mon May 12 16:03:00 CEST 2014
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 at 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 at 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 at 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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