This is a bioinformatics question involving R. I am a new bee in R and Bioconductor. I am a new bee in R and Bioconductor. I have a .gpr file from GenePix experiments. I want to load this file using marray package of Bioconductor and extract the foreground and background median values from the Cy5 and Cy3 channels. I was able to load the file. But need help in extracting the above mentioned subset of data.
Most of the samples I see on the internet are based upon the swirl dataset, which is loaded when marray package is loaded automatically. I don't see any sample where a .gpr file is processed.
It's better to ask Bioconductor questions on the Bioconductor mailing list (no subscription required) rather than cross-posting (which is frowned upon!) to StackOverflow and Biostars. From looking at the help page
class?marrayRaw I think you can extract, e.g., green background intensities as a plain old matrix and calculate per-sample medians with
apply(maGb(dat), 1, median)