Dear Eugene,

I think you might be able to find some useful functions that work on
one-channel arrays in the package aroma.light (e.g.
normalizeQuantileSpline).  You also should have no problem narmalizing your
data with vsn.  Also, some of the functions in the limma package demand two
channels but they seem to treat the different channels independently (e.g.
backgroundCorrect and normalizeForPrintorder).   I made a few changes to
some of these functions and got them to operate on single channel data.  I
am not a skilled or experienced programmer but these were minor changes and
the functions seem to be working properly.  I would be glad to send them to
you to use at your own risk.
:-)

Cheers,
Artur Veloso

On Thu, May 15, 2008 at 6:19 AM, Wolfgang Huber <huber@ebi.ac.uk> wrote:

>
>
> 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
> arrays.
>
> 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
> these.
>
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> 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@student.ucr.edu
> >  Dr. Frances Sladek Lab
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
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