[BioC] Limma: background correction. Use or ignore?

[Gordon K Smyth]

On Tue, April 4, 2006 11:58 pm, J.delasHeras at ed.ac.uk wrote:
>> But in my lab, we always background correct. There are a lot
>> of reasons for this. For one thing, foreground-background plots
>> almost always show that background correcting does remove some
>> systematic bias.
>
> what do you mean exactly by this? what's teh source of this bias?
> dye-specific bias?

For each channel on each array, plot log-foreground vs log-background.  E.g.,

  plot(log2(RG$Rb[,1]),log2(RG$R[,1]),pch=".")
  abline(0,1,col="blue")

If background is worth removing, you should see an increasing trend.

This is not dye bias.

Gordon