Download and Install
Zip-file with all the source code
For convenience, all the source codes described below are stored in the following zip-file
Structure of the data
The data is assumed to be stored as a data frame “Data” in a Rdata-file “Data.Rdata”.
The data frame “Data” has five columns
================ =================== Data$peptide : name of the peptide Data$protein : protein it belongs to Data$Rep : number r of the repetition Data$Trait : number t of the traitment Data$LogI : log-intensity for the peptide
An example of such data frame is provided in the demo
Building the priors
The building of the priors is based on a preliminary fit of the OneP model with the R-package “nlme”.
The R-source code for this step is:
(this step requires the R-libraries nlme and gdata)
NB: lme may not converge for a few proteins, in which case these proteins must be removed for this step (only).
The model for JAGS is specified by the file model.txt
The JAGS-source code for launching the computation is scriptJAGS.txt
Analyzing the results
Finally, the following R-source code computes from the output of JAGS the estimated protein abundances in the AllP model:
This code also performs the differential analysis decribed in the technical brief.