Description

This R notebook accompanies the MIC workshop: Modern data analysis in R/RStudio. It contains placeholders (...) to fill the code in exercises presented during the workshop.

You can knit this document into an HTML file. Once you fill in the code, change the parameter eval=F to eval=T in every code snippet. This way, the output of every code section will appear in the notebook.

R primer

The R for data Science book and the accompanying website is an excellent resource to get acquainted with R and its applications to data science.

Here is an introduction to data.table package that we use extensively in this analysis. Some advanced tips and tricks with data.table are covered here.

Data description

Data come from a microfluidic experiment where PC-12 cells were stimulated with 3 different growth factors (EGF, NGF, FGF2) at different concentrations. It comes from our recent publication Temporal perturbation of ERK dynamics reveals network architecture of FGF2-MAPK signaling (2019) available here.

The microfluidic device has four separate channels, thus 4 different treatments can be performed in a single experiment.

The PC-12 cells express a FRET biosensor to indicate activity of the ERK kinase.