[BioC] Background correlation with different scanners

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Fri Jun 2 02:59:13 CEST 2006

This is not a BioC issue in itself, but I thought some people might 
find it interesting.

I was using the 'cor' function to get correlation coefficients for the 
slides (2-colour cDNA) in some experiments I am analysing, and I found 
an interesting (to me, at least) difference in the background 
correlations that seems related to the scanner used.

I got the coefficients comparing both foregrounds, both backgrounds, 
and each foreground to its background. Both foregrounds show a high 
correlation in all my slides, indicating that most genes do not change, 
as expected. The foreground/background correlations are low... which is 
good too, but the actual numbers vary acording to the scanner used.

The slides that were scanned with an ArrayWorx scanner give 
coefficients around 0.10-0.15.
Those that were scanned with a Perkin Elmer ScanArray 5000 give me 
coefficients of around 0.03-0.10.
Finally, those scanned with an Axon 4200 give me coefficients of 0.01-0.04.

I always thought the background was best on the Axon ones, although the 
signals seemed "nicer" on the ArrayWorx. Hmmm...

That's all.


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
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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