I have no background training in programming and R, and I'm doing microarray analysis on my own. I find maEndToEnd to be a very helpful guiding source. However, my specific data set consists of normal tissue, cancer tissue, secondary lung and liver cancer, and healthy liver and lung tissues, and a couple of other types. If I treat this as a single study it skews the arrayqualitymetrics and other QC plots I want to on top of doing all the plots on the microarray study as a whole, make groups, especially for PCA plots. Not to mention that my data set as a whole is so large that most QC plots are unreadable. But, I can't seem to find a function that would return a separate data sheet for experiments based on their phenoData. For example, either the names of the GSMXXXX, or the histology, or anything, that would group the data in separate sets. If anyone could help me at all, I would be forever grateful.
Thank you.
