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Eugene Bolotin
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30
@eugene-bolotin-2112
Last seen 10.3 years ago
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