[BioC] RE: Advice on print-tip normalization

[Ramon Diaz-Uriarte]

Dear Mark and Gene,

With regards to the periodicity the "Print-order normalization of cDNA 
microarrays" by Gordon Smyth 
(http://www.statsci.org/smyth/pubs/porder/porder.html)
could be of interest.

I do have observed sometimes these print order effects here, and have used the 
approaches suggested in Smyth's document.

Best,

R.

On Wednesday 22 September 2004 15:11, 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.
>
> Such an effect ought to produce the periodicity you comment on below.
>
> Has any one else noticed a similar phenomenon?
>
>
> Regards
>
> Mark
>
>
> Date: Fri, 17 Sep 2004 10:32:33 -0700
> From: Gene Cutler <gcutler at amgen.com>
> Subject: [BioC] Advice on print-tip normalization
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324 at amgen.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hello.  I've just started using the marray package for processing a set
> of spotted oligo arrays.  The arrays, when intensities or log ratios
> are plotted against probe number, show a clear pattern of
> rising/falling values with a periodicity equal to the grid block size
> (~3600 spots).  I can see a similar periodicity in the printTip
> boxplots generated with marray.  Running printTipLoess smoothes out the
> boxplot nicely (and the MA plot also looks much nicer), but,
> surprisingly, when I export the normalized values and plot them against
> position, the grid block periodicity is little changed.
>
> I've tried different span values for the printTipLoess as well as
> trying with or without scaling (e.g. printTipMAD), but nothing I do
> seems to have much effect on this data artifact.
>
> Does anyone have any suggestions?
>
> Thanks.
>
> --
> Gene Cutler
> Research Investigator
> Bioinformatics
> Amgen SF
>
>
>
> Mark Reimers,
> senior research fellow,
> National Cancer Inst., and SRA,
> 9000 Rockville Pike, bldg 37, room 5068
> Bethesda MD 20892
>
>
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>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)