[BioC] normalisation assumptions (violation of)

[J.delasHeras at ed.ac.uk]

Hi,

I have a set of data from an experiment where there appears to be an 
effect of the treatment on a large number of genes. I put scatterplots 
for 6 of the slides here:

http://mcnach.com/MISC/scatterplots.gif

these are Cy3 vs Cy5, in log scale.

These show that many genes are differentially expressed, and they are 
mostly one one side only (upregulated; some of those slides are dye 
swaps).

Would this appear to violate (too much) any of the assumptions made by 
loess normalisation? Should I investigate other normalisation 
procedures?

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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