hi Yoong,

It appears that DEAnatomy is not a matrix of integers but factors.
DESeqDataSetFromMatrix()
is expecting a matrix of non-negative integers for the 'countData' argument.

you can explore with:

class(DEAnatomy)
str(DEAnatomy)
head(DEAnatomy)

Can you provide the code you used to make or import DEAnatomy?

Mike


On Wed, Mar 5, 2014 at 7:34 PM, FeiYian Yoong <fyoong@ucdavis.edu> wrote:

> Hi Mike,
>
> I am not sure what you are asking for. I tried any( DEAnatomy < 0 ) and I
> got a warning message
>
> Warning message:In Ops.factor(left, right) : < not meaningful for factors
>
> Please clarify your question so that I can provide you with relevant information.
>
> Many thanks,
>
> Yoong
>
>
>
> On Wed, Mar 5, 2014 at 9:22 AM, Michael Love <michaelisaiahlove@gmail.com>wrote:
>
>> 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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