Hi, I have inherited a set of single-dye (R) gpr, and need to process them via limma. After several tries, managed to load via read.maimages and backgroundCorrect using dummies values for G and Gb from R and Rb, respectively. Two questions: A) Am I right to say that normalizeWithinArrays for single-dye gpr ? B) How to normalize between arrays in the right way ? Should it be normalizeBetweenArrays(RG, method="quantile") or normalizeBetweenArrays(RG$R, method="quantile") or something else ? [[alternative HTML version deleted]]

Check out this previous thread from the mailing list: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 8032 /match=read+single+channel+genepix+limma+analyze+miRNA+experiment There are other previous threads that you will find useful too if you try searching the mailing list: http://dir.gmane.org/gmane.science.biology.informatics.conductor -Paul On Mon, Jun 2, 2008 at 11:25 AM, Ng Stanley <stanleyngkl at="" gmail.com=""> wrote: > Hi, > > I have inherited a set of single-dye (R) gpr, and need to process them via > limma. After several tries, managed to load via read.maimages and > backgroundCorrect using dummies values for G and Gb from R and Rb, > respectively. Two questions: > > A) Am I right to say that normalizeWithinArrays for single-dye gpr ? > B) How to normalize between arrays in the right way ? Should it > be normalizeBetweenArrays(RG, method="quantile") or > normalizeBetweenArrays(RG$R, method="quantile") or something else ? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >