[BioC] BioC normalisations for small array 2 colour data?

[Dan Swan]

Hi,

I have some data from a small specialised microarray - 200 genes, 1
spiked control, 1 negative control.  This is 2 colour data, with dye
swaps.  I was wondering what an appropriate normalisation for this
scenario is within Bioconductor given that Lowess is unreliable for
<1000 genes?

Any pointers would be gratefully recieved.

thanks,

Dan

-- 
Senior Research Associate, Bioinformatics Support Unit,
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
University of Newcastle upon Tyne,
Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253  (Leech offices: Rooms M.2046/M.2046A)
Tel: +44 (0)191  246 4833 (Devonshire offices: Rooms G.25/G.26)
Website: http://bioinf.ncl.ac.uk/support/