For starters, read Hadley Wickham’s and Garrett Grolemund’s great book, R for Data Science. This is a modern, well-written book (available online free) that’s easy to follow and will get you going in the right direction! It is not specific to cytomics, but is a great starting point nonetheless.
Finding help online
Bioconductor’s help site – full of great tutorials, links to videos, and message board for more complicated questions.
Bioinformatics questions – bioinformatics questions not pertaining to a specific R package are best addressed on Biostars
Programming questions – try StackOverflow
Getting help without ever leaving RStudio
Help within R – R has a comprehensive help system built right in! Type ‘?FunctionName’ right in the R terminal (no quotes and replace FunctionName with the name of the function you need help with, or click on the ‘help’ tab in RStudio.
Locate and read vignettes. These are often extremely informative, and you can follow along, working examples they give. For example, check out the flowCore vignette, or the flowFP vignette.
sample datasets – type ‘data()’ to see all available sample datasets for the packages you have loaded. These can be extremely useful when learning to use new packages.