Question: (Closed) Explanation of Limma logFC calculation
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gravatar for John S.
11 days ago by
John S.10
John S.10 wrote:

Hi guys,

I have a doubt regarding the logFC calculation in limma. I searched for the answer in Biostars but I have not found anything that help me to understand my doubt. Supposedly logFC is: LOG2(mean (Group A) / mean (GroupB)) Meaning that if a gene logFC has an expression of 50 in Group A and 100 in Group B, the log2 FoldChange would be -1. Thus, the gene would be two times more expressed in Group B. However, I have checked the logFC that appears in the topTable obtained with the functions in limma and the logFC seems to be something else. Here, the logFC represents the difference between the mean of the groups. The value is then elevated to 2 and log transform, to address correctly the difference between the groups. Thus, the value indicates directly the difference between the two groups, it is not the ratio between the groups. So, it is the value of the topTable a proper logFC? Or should I calculate the logFC manually? Maybe I am confused with the terminology and the value of limma is called something else or the "supposedly logFC" that I addressed is named differently.

Thank you for your precious time.

ADD COMMENTlink written 11 days ago by John S.10

Can you give references or links where you found

I have checked the logFC that appears in the topTable obtained with the functions in limma and the logFC seems to be something else

With only words it is difficult to understand what you mean.

ADD REPLYlink modified 11 days ago • written 11 days ago by ATpoint26k
1

I just realized my mistake. I was dividing values that were log transformed, thus, I should have done a subtraction instead. By doing so, I have the same results that limma does. Meaning that here the logFC is directly the difference between the groups rather the ratio (since the values are log transform). Thank you for your quick answer.

ADD REPLYlink written 11 days ago by John S.10

Hello John S.!

Solved by OP.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 11 days ago • written 11 days ago by ATpoint26k
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