[BioC] scanner effects

[Christopher Wilkinson]

I have a question regarding the effect of different scanners on 
cDNA slides.

I have data for a small (8 slide) microarray experiment.
These slides were hybridised and scanned at another facility, and
for reasons that are not quite clear to me, were scanned again once
our local facility was up and running.

Based on the MA plots, it appears the gain was turned up on the second set of 
scans wrt the first. The first scan has a distinct red dye bias at low 
intensity, whilst the second scan has a smaller green dye bias, and larger 
intensities (avg intensities start at 2^7 vs 2^6 and max intensities are 
higher).

With regard to the analysis, I'm not sure how to rate one set of scans over 
the other. I've analysed each seperately, and also combined them treating the 
different scans as technical replicates.

I figure that the different scans are highly correlated technical replicates - 
very similar to the case of using adjacent duplicate spots. To test this out I 
created an MA object from getting normalised MA objects from the two scans and 
then combining them so I had an array with twice the normal number of spots 
and with adjacent spots representing the same cDNA, but different scans.  This 
allowed me to use the dupcor.series function of limma to estimate the spatial 
correlation (about 0.32 with IQR from of (0,0.6)) to use in gls.series. 
However given that background is different between the slides I'm not sure if 
this approach is really that valid.

I've also looked at the overlap of the top50 genes (ranked on interaction 
parameter) from each analysis 
scan 1 vs 2 = 28
scan 1 vs combined = 28
scan 2 vs combined = 42
scan 1 vs scan2 vs combined = 44

Essentially I'm interested in opinions on how to handle the problem of which 
scan to use.  I can arbitrarily (or randomly) use one of the scans, but I was 
wondering if anything can be gained from the use of two physically different 
scanners (or have I just picked up another source of variation)...

Cheers
Chris

Dr Chris Wilkinson

Research Officer (Bioinformatics)        | Visiting Research Fellow
Child Health Research Institute (CHRI)   | Microarray Analysis Group
7th floor, Clarence Rieger Building      | Room 121
Women's and Children's Hospital          | School of Applied Mathematics
72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005

Math's Office (Room 121)        Ph: 8303 3714
CHRI   Office (CR2 52A)         Ph: 8161 6363

Christopher.Wilkinson at adelaide.edu.au

http://mag.maths.adelaide.edu.au/crwilkinson.html