[BioC] Limma; Background and Single Channel Analysis

[J.delasHeras at ed.ac.uk]

Quoting Simone de Jong <dejong_simone at hotmail.com>:

>    Third,  I  have  been experimenting with several background correction
>    methods.  It turns out that 'normexp' gives good results for most, but
>    not  all arrays. Two of them look really weird, with the MA cloud only
>    starting  after  5.. I came to the conclusion that the method Subtract
>    results  in the best looking MA plots for all of my arrays. The 'half'
>    and 'minimum' method do not give such good results, with ugly stripes.

Have you also tried 'none', no background correction at all?
I have recently found that some of my slides give much better results 
if I do not correct for background. The slides are very clean with very 
low background and good signals. It turns out that the slides that 
benefited the most from background correction wre all scanned with an 
ArraywoRx scanner, and the other ones were scanned with an Axon 4200AL, 
so it can be largely a scanner-dependent effect (I haven't pursued this 
because the ArraywoRx one is in another building so I just use now the 
one closest to me, two floors down).
Maybe it does nothing to you, but if your slides are all similar (hybs, 
scanner, etc) maybe 'none' will be the best option. Give it a try if 
you haven't yet.

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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