Clarification on the fold change cut off...

[sharvari14]

Hi,

I am using this package to generate an MA plots and label gene names using the default padj and logFC thresholds. On running the function, I see that in the source code the condition for logFC to determine significance level is: abs(data$log2FoldChange) >= log2(fc)

Can you please help clarify if the FC value is log transformed? Or, based on linear scale?

Thanks Sharvari