[BioC] Re: Advice on print-tip normalization

Adaikalavan Ramasamy 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
> Bioinformatics
> Amgen SF
> 1120 Veterans Blvd.
> South San Francisco, CA  94080
> (650) 244-2489
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