Current release is 0.11.
Release 0.11 contains a bug fix for file chipVarEstepCMu.m
Release 0.1 is the first release associated with the paper, containing scripts for recreating the results given.
The toolboxes required to run the code are listed below.
Finally you will also need the NETLAB toolbox in your path.
demSpellmanVarwhich run the code on the metabolic and cell cycle data sets. Also of interest may be the script
demFakeVarwhich runs the code on artificial data.
demSpellmanVarinvoke the functions
chipVarEMrespectively which compute the posterior estimates of the latent variables by maximising the variational lower bound on the likelihood. The functions used are different as there is no need to estimate the baseline expression level for cDNA array data such as the cell cycle data set. The scripts output a variable model, containing the parameter values which maximise the likelihood, and expectationsB (posterior expectations of the regulatory intensities) and expectationsC, posterior expectations of the protein concentration profiles. The function
chipVarEMmualso outputs a variable expectationsMu containing posterior statistics for the distribution of the baseline expression levels. The variable expectationsC has four fields: .entropy, a number contatining the posterior entropy of the approximating distribution, .c, a matrix with as many rows as transcription factors and as many columns as time points, .ccT, a 3D array containing the correlations among transcription factors at each time point, and .cAltc, a 3D array containing correlations among transcription factors at consecutive time points. By specialising the transcription factor index one can obtain plots of the transcription factor protein concentrations with errorbars. An example is show below for the transcription factor ACE2 during the cell cycle.
expectationsB.errorbarscontains the associated error bars. By specifying to a transcription factor, we can obtain a distribution of the significance levels of its regulatory intensities. An example of this is shown below for the transcription factor ACE2 during the cell cycle.