[BioC] OT: Problems with Nimblegen scans?

Alicia Oshlack oshlack at wehi.EDU.AU
Wed Jun 27 12:52:32 CEST 2007

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.


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";
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> 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

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