[BioC] RE: Advice on print-tip normalization

[Gordon K Smyth]

Spots in a given position within a print-tip group are always printed from
the same 384-well plate of DNA.  Genes of similar function or homology
are often grouped together on a plate.  If there are systematic differences
between plates due to the nature of the probes, this would lead to periodicity
through the print-tip groups, but you certainly don't want
to remove this structure in the normalization.

Gordon

> 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
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>