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

Eugene Bolotin ybolo001 at student.ucr.edu
Tue May 13 23:32:21 CEST 2008

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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