how do the DEG tools work ?

I have a question about limma or edgeR or any other DEG tool. how the tool calculate the treat and control fold changes? for example in the first section we put control and second treat. So is it Control-Treat(in fold changes) or Treat-Control
it is just about how the DEG tool calculate fold change result

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Hi @amir,

it should be Control-Treat in your example.

ping @mblue9 as well.

Sorry for the late reply!

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Actually, for the limma and edgeR tools at least, I think you want Treat-Control. Control-Treat would be if you want to know what genes are up/down in the control relative to the treatment. Usually people want to know what’s up/down in the treatment relative to the control. Even if you input the Control sample count files first and the Treat counts files second, it’s the contrast order that specifies how the groups are compared. See the help section in the limma tool form (e.g. for Mut-WT the fold changes in the results will be up/down in Mut relative to WT).

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