[BioC] Re: Advice on print-tip normalization
ramasamy at cancer.org.uk
Fri Sep 24 03:48:22 CEST 2004
Probably a stupid suggestion but here goes.
It seems like differing amount of probes are being deposited
systematically. So, is there a way to check if your print tips are all
level or the spotting/washing well which the print tip comes in contact
with is level as well ?
On Thu, 2004-09-23 at 17:27, Gene Cutler wrote:
> On Sep 22, 2004, at 6:11 AM, Reimers, Mark (NIH/NCI) wrote:
> > Hello Gene,
> > I don't have any advice but some related observations based on looking
> > at regional biases on spotted microarrays. In the slide data that have
> > come in, there seems often to be a bias toward red on the top and
> > bottom edges of the print-tip groups, and a bias toward green in the
> > middle of the print-tip blocks. No explanation occurs to me, but this
> > effect is apparent on most of the arrays. One of our collaborators
> > claims the effect disappears with a more effective washing treatment,
> > but hasn't sent slide images.
> What I'm seeing are largely overlapping periodicities in both channels.
> The intensities start low at the beginning of a block, peak in the
> middle, and go down again at the end. This repeats in each of the 48
> blocks across the slide, getting more exaggerated across the array.
> This is accompanied by a greater scatter in the intensity ratios, with
> much more noise in the center of the grids, where both channel
> intensities are highest.
> Gene Cutler
> Research Investigator
> Amgen SF
> 1120 Veterans Blvd.
> South San Francisco, CA 94080
> (650) 244-2489
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor