[BioC] Error message with DESeqDataSet

[Yoong [guest]]

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

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