Question: DeSeq2: Use negative numbers and fractions
0
gravatar for rraadd_8
2.9 years ago by
rraadd_80
rraadd_80 wrote:

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 • 550 views
ADD COMMENTlink modified 2.9 years ago by Michael Love25k • written 2.9 years ago by rraadd_80
Answer: DeSeq2: Use negative numbers and fractions
2
gravatar for Michael Love
2.9 years ago by
Michael Love25k
United States
Michael Love25k wrote:

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.

ADD COMMENTlink written 2.9 years ago by Michael Love25k

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

ADD REPLYlink written 2.8 years ago by rraadd_80
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