[BioC] RE: Advice on print-tip normalization

Reimers, Mark (NIH/NCI) reimersm at mail.nih.gov
Wed Sep 22 15:11:18 CEST 2004


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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