Log fold change

[Erwan]

Hi there,

I've seen recently in some differential expression tools (like Deseq) that the fold change is calculated with a logarithmic scale rather than a "regular" one, and I can't see why.

Is this for technical purpose, like plotting graphs, or is there another reason ?

Thanks,

Erwan

[Kaas]

Hi Erwan

it is log2-fold change and the reason is to be able to look at data spanning several order of magnitude (from ~10 reads per gene in one to 500.000 reads per gene in another gene). you can say that this is more important for the expressions levels than for fold change but i think you mainly do this because of plotting an avoiding a few outliers to overtake the plot.

[mastal]

Fold change is a ratio. If it wasn't plotted as log(fold change), cases of downregulated expression would all be between 0 and 1, whereas upregulated expression could have any value between 1 and infinity.

Log2 is used because that way a two-fold increase in expression (for example) has a log2(fold change) value of +1, while a two-fold decrease in expression has a log2(fold change) value of -1.

[Erwan]

Wow, I did not think about that but it seems obvious now that you explained it.

Again, thank you very much for these really clear explanations.

Bye.

Erwan