Hi,
I am working on Agilent Two-Colour RNA Microarray. I would like to analyze the results as SIngle-Colour. I have the data from the analysis, which were already normalized with LOESS.
I would like to normalize the data using the Shift to 75th Percentile method in limma package. I know that normalizeBetweenArrays has a option to normalize using sclae method, but how can I know or change the scale value?
Thanks

Please do not re-normalize two-color data that has already been loess normalized, except by the Aquantile method. See this paper for suggested practice:

  http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-165

My lab has not used scaling normalization for two color microarray data for 15 years, and the 75th percentile method in particular is not appropriate, which is why it is not offered as an option in the limma package.