[BioC] Fwd: Question about normalizing one color Agilent array using loess

Wolfgang Huber huber at ebi.ac.uk
Thu May 15 12:19:04 CEST 2008

Dear Eugene,

marray's and limma's so-called loess normalisation aim to adjust for
trends in the log-ratios (M) as a function of the log geometric mean
intensity (A), but are not designed to deal with spatial trends on your

You will need to decide whether the data is worth trying to adjust for
such spatial trends computationally, by some other means, or whether you
call it a data quality problem and address it by improved experimental
procedures. Other people may be better qualified to advise on either of

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

13/05/2008 22:32 Eugene Bolotin a écrit
> Dear Bioconductor,
>  I am running a protein binding microarray experiment(PBM). In this
>  experiment protein is bound to double stranded microarray and
>  visualized using antibody (red fluorescence). Basically this gives you
>  a one color Agilent (gpr) microarray file with an additional gal file.
>  I tried using loess and other normalizations on this setup using
>  bioconductor, limma and marray package. I have run into some problems.
>  One is the importing problem, which I solved using dummy column for
>  green spectrum. The other problem is that all the normalization
>  schemes in Limma and  marray require a "two color" array. Does anyone
>  know how to run normalization with just one color. My main problem is
>  uneven fluorescence across the array. One side seems noticeably
>  brighter than the other, and I want to even it out somehow, loess is
>  supposed to do it.
>  Thanks a lot
>  --
>  Eugene Bolotin
>  Ph.D. candidate
>  Genetics Genomics and Bioinformatics
>  University of California Riverside
>  ybolo001 at student.ucr.edu
>  Dr. Frances Sladek Lab
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