multi PMT scan combination
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@miroslava-cuperlovic-culf-108
Last seen 9.9 years ago
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@henrik-bengtsson-4333
Last seen 9 weeks ago
United States
Hi. References: [1] H. Bengtsson, J. Vallon-Christersson and G. J?nsson, Calibration and assessment of channel-specific biases in microarray data with extended dynamical range, BMC Bioinformatics, 5:177, 2004. Scanning: "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 Henrik 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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@matthew-scholz-1563
Last seen 9.9 years ago
Hi Mira, If I understand you correctly, you wish to merge datasets obtained from doing multiple scans of the same set of slides. The best treatment I've read about this was in: Piepho et al. (2006) Combining signals from spotted cDNA microarrays obtained at different scanning intensities. Bioinformatics (January 17, I think). Their approach is implemented in SAS and they will email you the code. If I recall correctly, the code is written for seven (!) repeat scans and not less. Unfortunately, I don't think it's available in R, and I'm nowhere near the programmer/mathematician who could do it. Nonetheless, the paper is worth reading. If someone else has better information, I'd like to hear about it too. Good luck, Matt 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 -- Matt Scholz Senior Research Specialist Department of Plant Sciences University of Arizona (520) 621-1695
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