[BioC] DEXseq ignoreRank

[Michael Love]

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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>