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

Gordon K Smyth smyth at wehi.EDU.AU
Tue Apr 4 23:10:47 CEST 2006

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.,


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

This is not dye bias.


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