[BioC] scanner effects
christopher.wilkinson at adelaide.edu.au
Wed Oct 8 18:45:17 MEST 2003
I have a question regarding the effect of different scanners on
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
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)...
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
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