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

================	===================
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:

BuildJagsFiles.R

(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).

Launching JAGS

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:

ALLP.R

This code also performs the differential analysis decribed in the technical brief.