Hello BioStars,
I'm rather new to analyzing microarray data, so please forgive my ignorance. I have a couple of questions.
Can I RMA normalize the probe data in my excel worksheet which contains on average 7 probes per gene and 3 technical replicates for each probe? If so, how? I have JMP Genomics. Not sure if I can do it with that.
Before finding out that RMA is one of the most common methods for converting probe level data into transcript abundance, I was going to Loess normalize the data then average all of the probes and technical replicates to get a single transcript abundance value for each transcript (corresponding to genes and intergenic regions). From what I've read though, it doesn't seem like people do this. Rather most people seem to RMA normalize their data and then average the technical replicates. Is that assessment correct?
I also have the Nimblegen array data files (e.g. .pair files) if it is necessary to go back to that level, and I found the following page which has a pipeline for this using R and bioconductor. I'm just not very good with these and I have limited access to a linux OS right now, so if there is an easier way with my Excel spreadsheet, I'd like to know that way. http://akka.genetics.wisc.edu/sandbox/groups/genetics875/wiki/7a793/attachments/03804/JYSgro_R-Bioconductor_2010.pdf?sessionID=eda971f6e06acc29ec6c9e10e3c767cf222044f4
Thank you,
Jason
