Dear John, Version 2.9.9 of the limma package (very recent) has a function mergeScansRG() which will merge two GenePix scans. In the next week or two there'll be a function for merging an arbitrary number of scans. Cheers Gordon At 10:00 PM 14/02/2007, bioconductor-request at stat.math.ethz.ch wrote: >Date: Tue, 13 Feb 2007 16:38:22 -0800 >From: John Fowler <fowlerj at="" science.oregonstate.edu=""> >Subject: [BioC] Combining data from scans at different intensities >To: bioconductor at stat.math.ethz.ch >Message-ID: <p06240803c1f80a6ca5dd@[128.193.138.53]> >Content-Type: text/plain > >Hello, > >I would like to use data extracted from images scanned at 3 different >intensities in our GenePix scanner. There are a couple of papers >that I could find (Lyng et al 04, Piepho et al 06) that describe >methods to combine these data and thus help deal with problems of >saturation and signals across the dynamic range of the scanner. > >I looked for a way to do this in bioconductor, and found a post from >Dr. Henrik Bengtsson, indicating that this was possible using the >aroma.light package in bioconductor. However, he indicated that this >should be done with data from scans in which the laser intensity =was >not changed=. > >Unfortunately, my scans used two different laser intensities. > >Does this invalidate using aroma.light for this purpose? Is there >any other Bioconductor package that could deal with my (apparently >incorrectly obtained) data? > >many thanks! >John > >-- >John Fowler Associate Professor >Botany and Plant Pathology (BPP) Dept. >2082 Cordley Hall Phone: (541) 737-5307 >Oregon State University FAX: (541) 737-3573 >Corvallis, OR 97331-2902 USA Email: fowlerj at science.oregonstate.edu