DeSeq2: Use negative numbers and fractions
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rraadd_8 • 0
@rraadd_8-11857
Last seen 7.0 years ago

Dear users,

Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions,

and I need to use DeSeq's statistics to find out significantly up/down genes.

Since for my data, min=-10 and max=10, I can convert it into counts by 

  1. first multiplying with a constant eg. 1000 to preserve the decimal precision.
  2. and then add some constant value eg. 10000 to make everything positive.

Would it hamper my analysis?

deseq2 logfoldchange • 1.8k views
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@mikelove
Last seen 4 hours ago
United States

You can't use negative numbers with DESeq2. The model only makes sense if the input is counts or estimated counts of reads or fragments.

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Thanks. I wonder if it is possible, (independent of DeSeq2) to use Wald test for negative numbers? 

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