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

[J.delasHeras at ed.ac.uk]

I have been using LimmaGUI for a while to analyse my cDNA microarrays. 
I have always used "substract" as a method for background correction. 
Why? Not sure. Intuitively it made sense, and I didn't observe any 
obvious problems.
Once I played with the different methods for background correction 
available in LimmaGUI, and when looking at the MA plots I decided I 
preferred to substract.

However, I have recently had problems with the statistics being quite 
poor in my analises (see my post a week ago or so about low B 
values)... and whilst checking the data, I noticed that at least in my 
current experiments, if I do no background correction at all the stats 
look a lot better, the MA plots look better, and everything looks 
better in general. The actual list of genes doesn't change a lot, but 
the values seem a lot tighter.

This makes me question whether we should background correct at all. My 
slides are pretty clean, low background. Am I not adding more noise to 
the data by removing background?

Can anybody point me to a good reference to learn about the effects of 
background correction, pros and cons? I'm just a molecular biologist, 
not a statistician, but I need to understand a bit better these issues 
or there'll be no molecular biology to work on from my experiments!

Jose


-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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University of Edinburgh
Edinburgh EH9 3JR
UK