How does limma calculate log-ratio of fold change?
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@moradzadeh_k921-10925
Last seen 5.1 years ago

Hello everybody

I faced a problem in analysis of the data set "GSE27274" by limma package. The parameter "Coef" which shows "logFC" calculated by limma  is different from the one I gained manually. I calculated log2 of treatment expression values average divided to control expression values average. I have not experienced this problem in analysis of other datasets. Is there any problem with my calculation?

Thank you

 

 

limma logfoldchange • 663 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Yes, there's a problem with your calculation. Assuming you are just comparing two groups, you need to log2 first, then average, not the other way around.

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