I did the protocol as Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks from the nature protocol. The online pdf is here
I have a question when i see Figure 8, as below,
I find the boundary between sig and no sig is around 2.5 on the left axis, its p-value is about 0.003. But i think it should be 2(p-value 0.01) or 1.3(p-value 0.05) on the axis.
I am confused by this figure and need some help.
Maybe the threshold is corrected for the multiple hypotheses being tested?
From a biological point of view, I'm wondering what is the interpretation of such a volcano plot? I mean, I find 'suspicious' that the DE genes show very low fold changes... (even on a log2 scale). Do you expect such pattern?
"Significant" in this case is based solely on the alpha (p) value. It's not suspicious, just completely arbitrary :)
Do you mean "Significant" is arbitrary? But i think they have use the wrong alpha value.
Yes to both of those :)