How to interpret the negative Log2FC from DESeq2 output?

Question

[Apex92]

Hi, I have a gene with log2fc = -1.67 when comparing KD and control conditions (bulk condition) using DESeq2. Now, I have another experiment condition where I want to set sample comparisons in a way that I get the same FoldChange of that particular gene, meaning I will choose KD samples vs Control sample in a way that mimics the same FoldChange as my previous experiment.

To know the actual FoldChange I am trying to convert the log2fc = -1.67 to FoldChange version of it. My question is should I consider the absolute number when converting negative log2fc to FoldChange or not? or it does not matter?

• If considering the negative value the FoldChange is: 2^-1.67 = 0.31.
• If considering the absolute value the FoldChange is: 2^1.67 = 3.18.

Which one I should proceed with? Any insight on this is appreciated.

Answer 1

[rsiaperas]

Short answer: the first, no absolute number

But you better check this comment to understand what fold change is how to calculate the log FC for -1.5 fold change?

or this longer thread Fold change - a final explanation