[BioC] Advice on print-tip normalization

Gene Cutler gcutler at amgen.com
Fri Sep 17 19:32:33 CEST 2004


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



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