How should I interpret FB_Plot in microarray analysis?

Question

[Nemo]

Hi,

I have a foreground-background plot using limma plotFB function for one array. I couldn't find any detailed resource of how to interpret this plot.

So what does the plot shows? what is the blue line here?

[Ram]

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Answer 1

[Gordon Smyth]

The documentation (?plotFB) says:

A foreground-background plot is a plot of log2-foreground vs log2-background for a particular array.

Each dot presents one point on the microarray.

The blue line is simply the line with x=y. The foreground should be equal to background plus signal, so the x=y line estimates the lower bound for the expected foreground values.