[BioC] multi PMT scan combination

Henrik Bengtsson hb at maths.lth.se
Wed Jun 14 16:45:47 CEST 2006


[1] H. Bengtsson, J. Vallon-Christersson and G. Jönsson, Calibration
and assessment of channel-specific biases in microarray data with
extended dynamical range, BMC Bioinformatics, 5:177, 2004.

"To calibrate signals for scanner biases, scan the same array at
multiple PMT-settings (in decreasing order) at three or more PMT
settings. Do this without washing, cleaning or by other means changing
the array between subsequent scans. Although not necessary, it is
preferred that the array remains in the scanner between subsequent
scans. This will simplify the image analysis since spot identification
can be made once if images aligns perfectly." [From help pages in the
aroma package]  It is actually enough with two scans, but the model
assumptions made in [1] cannot be verified from your data.

In R:
library(aroma.light)   # From http://www.braju.com/R/
# For each array and channel, put all K scans as columns in a matrix
yR <- calibrateMultiscan(yR)   # yR : NxK matrix
yG <- calibrateMultiscan(yG)  # yG : NxK matrix

I normally ignore background signals in my analysis.  Howeer, if you
wish to include them in your calibration, I recommend you to calibrate
them together with the foreground signals, because the scanner does
not differentiate between foreground and background anyway.

Alternatively, if you use the higher-level 'aroma' package, for
instance to read GPR files etc, you may read each array into an RGData
object 'rg' and call 'calibrateMultiscan(rg)' to do the above.

Finally, if you use BASE [http://base.thep.lu.se/], just install the
aroma.Base package and there is a multiscan calibration plugin ready
to be used (same algortihm as above).

Hope this helps


On 6/13/06, Miroslava Cuperlovic-Culf <miroslavac at health.nb.ca> wrote:
> Dear All,
> Has anyone set up scripts to combine multi PMT readings (multiple gpr files
> for the same slide)?
> Help and information would be highly appreciated,
> Sincerely,
> Mira
> __________________________________________________________
> Miroslava Cuperlovic-Culf, Ph.D.
> Research Scientist
> Institut atlantique de recherche sur le cancer/Atlantic Cancer Research
> Institute
> 35 Providence, Moncton NB
> E1C 8X3 Canada
> (506) 862-7512 (tel) (506) 862-7571 (fax)
> www.canceratlantique.ca / www.atlanticcancer.ca
> Atlantic Microarray Facility www.atlanticcancer.ca/amf
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