First-time R user here. I struggled with getting the R package XenoCat working, here I describe how I got it to work, and some of the pitfalls along the way. The XenoCat package, created by Laajala et al. is a tool for statistically analyzing xenograft treatment experiments. See Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo.
I followed instructions in the instruction PDF from the XenoCat page, and downloaded the current version of R (3.2.0) from the R project homepage. The command in the instruction document to install the packages from the R command line was unclear, and kept throwing errors. I tried unzipping the XenoCat and other packages manually into the library sub folder in the R installation folder. This is not the same as installing, apparently.
Eventually I looked in the R FAQ and found that from the R GUI there is a Packages menu that installs packages. I selected and installed the dependent lme4 package, then selected the locally downloaded XenoCat_1.0.3.zip package. When I tried to access the XenoCat library, it told me it was built before R 3.0.0, and to reinstall it.
I was able to find a previous version of R that XenoCat was tested in (2.14) on the previous releases of R page, and after installing it and repeating the installation of the lme4 and XenoCat packages through the Packages menu in the GUI, it seems to be working.
I am leaving out many other stupid attempts I tried to get this to work, so I hope this document might help some other first-time R users get started with it. I frequently run into the problem of new jargon with new software that creates a significant barrier to entry.
