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Old 03-24-2014, 07:06 AM   #1
Erwan
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Location: Nantes, France

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Default Log fold change

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
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Old 03-24-2014, 09:15 AM   #2
Kaas
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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.
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Old 03-24-2014, 12:12 PM   #3
mastal
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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.
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Old 03-25-2014, 05:05 AM   #4
Erwan
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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
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