What do you get for:

any( DEAnatomy < 0 )
On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote:

> Hi Mike,
>
> Hre you go:
>
> > sessionInfo() R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] DESeq2_1.2.6            RcppArmadillo_0.3.920.3 Rcpp_0.10.6
> [4] GenomicRanges_1.14.3    XVector_0.2.0           IRanges_1.20.6
> [7] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.40.0      AnnotationDbi_1.24.0 Biobase_2.22.0
>  [4] DBI_0.2-7            genefilter_1.44.0    grid_3.0.2
>  [7] lattice_0.20-23      locfit_1.5-9.1       RColorBrewer_1.0-5
> [10] RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2
> [13] survival_2.37-4      tools_3.0.2          XML_3.98-1.1
> [16] xtable_1.7-1
>
>
> Thank you,
>
>
> Yoong
>
>
>
>
> On Tue, Mar 4, 2014 at 7:33 PM, Michael Love <michaelisaiahlove@gmail.com>wrote:
>
>> Hi Yoong,
>>
>> The test that prints this error is simply:
>>
>> if ( any( counts(object) < 0 ) )
>>     return( "the count data contains negative values" )
>>
>> What do you get for:
>>
>> any( DEAnatomy < 0 )
>>
>> Can you include the output of sessionInfo() ?
>>
>> Mike
>> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote:
>>
>>>
>>> Hi Mike,
>>>
>>> I have a small technical question. I kept getting this error message
>>> when I tried running a DE with DESq2 (version 1.2.6):
>>>
>>> DESeqDataSet(se, design = design) :
>>>   some values in assay are negative
>>>
>>> It does not make sense to me because there is no negative values in the
>>> dataset (gene count). Please explain.
>>>
>>> Thank you,
>>> Yoong
>>>
>>>  -- output of sessionInfo():
>>>
>>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = colData,
>>> design = ~genotype+time+temp)
>>> Error in DESeqDataSet(se, design = design) :
>>>   some values in assay are negative
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
>>
>

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