[BioC] Combining data from scans at different intensities

[Gordon Smyth]

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