I'm learning to analyze GEO data and using GEO2R is the most straightforward to me, but I'm having problem understanding how GEO2R (or limma) calculate the logFC.
I read this link https://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R and noticed this:
"First define the treated group (it will be colored in blue), then define the control group (it will be colored in pink). The order is important for calculating log fold changes later in the analysis"
The result looks like this https://ibb.co/CKdRkSz
It seems to me that logFC is calculated in GEO2R as logFC = log(control/treated) (or log(normal/tumor) in this case) However, I've read from several sources that logFC = log(treated/ control)
This is confusing me in interpreting gene expression level. Could you please help explain this to me.
Thank you very much.