Hi list, this is not strictly BioC, but I know there is quite a few people here using Nimblegen arrays. Has anybody else experienced problems with their scans? In particular, I received data that was scanned with settings giving rise to a significantly larger amount of saturated features than expected/wanted. We had done an experiment comprising 4 hybs, in triplicate (12 chips). The first batch was very good (well, except from a duff hyb... which they didn't tell me, and only when I started enquiring -my data looked weird- they acknowledged the problem and re-hybed it). But the past month we did the other two sets, and their scans are too strong. Anybody else? Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

Hi Jose, We experienced a similar thing with our custom Nimblegen arrays. We asked them to rescan the arrays again at a lower setting which improved things a bit but we still had some saturated probes. Cheers, Alicia Alicia Oshlack, PhD Division of Bioinformatics Walter and Eliza Hall Institute > Message: 15 > Date: Wed, 27 Jun 2007 01:51:18 +0100 > From: J.delasHeras at ed.ac.uk > Subject: [BioC] OT: Problems with Nimblegen scans? > To: bioconductor at stat.math.ethz.ch > Message-ID: <20070627015118.97eaqyxvk0ggo808 at www.staffmail.ed.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > > Hi list, > > this is not strictly BioC, but I know there is quite a few people here > using Nimblegen arrays. > Has anybody else experienced problems with their scans? In particular, > I received data that was scanned with settings giving rise to a > significantly larger amount of saturated features than expected/wanted. > We had done an experiment comprising 4 hybs, in triplicate (12 chips). > The first batch was very good (well, except from a duff hyb... which > they didn't tell me, and only when I started enquiring -my data looked > weird- they acknowledged the problem and re-hybed it). But the past > month we did the other two sets, and their scans are too strong. > > Anybody else? > > Jose > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 > Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK > >