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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