Biometry Research Group

Statistical Software

Finding Biologically Relevant Response Patterns in High-throughput Experiments

(Software written by Stuart G. Baker)

The program requires Mathematica 8 .

To run provided example:

copy all files into some folder "FOLDER"
start a new Mathematika session
evaluate SetDirectory["FOLDER"]
evaluate << mfit.m
evaluate MFit[dataset]

To try on your own data:

format the data as follows.

dataset={dataname, data,geneid,genename,times,numsamples}, where
dataname= name of data set
dataset = a matrix of gene expression levels
rows indicate genes
columns 1 to 6 with 3 times and 2 samples: indicates (1,2,3,1,2,3),
geneid= a list of gene ID's,
genename = a list of gene names,
times= list of times of analysis,
numsamples = number of samples per time*)

First time on your data evalutate

MFit[NewFit->True, NameNew->"name1", NameStore->"name2"]

Second time on same data evaluate

MFit[NewFit->False, NameStore->"name2"]

In general evaluate MFit[dataset,options] , for example where the options are

ParameterNames::usage="names of symbolic parameters"
ModelSet::usage="set of models to fit; default is All "
NewFit::usage="True or False (default)"
ShowReport::usage="True or False (default)"
Replicate::usage="True (default) or False for three replicates"
NameNew::usage="name to create if NewFit->True"
NameStore::usage="name to retrieve if NewFit->False"
PickGene::usage="True means to fit particular genes; False otherwise"
GeneT::usage="list of particular gene ids to fit"

To reproduce the data analysis in the paper, type
dataset1=GenDataX[1,1];
MFit[dataset1, NewFit->True, NameNew->"name1", NameStore->"name2];
where you pick "name1" and"name2"
This should take 1-2 hours to run.

Downloads

Download All (zip, 3.82mb)

mfit.m	main program and calls all programs
mfitcomp.m	computes Criteria
mfitreport.m	reports AIC for all genes
mfitgene.m	fits each gene using core fitting program
mfitcore.m	core fitting program
mfittest.m	fit hypothetical test data
mfitdata.m	generate data in correct format from raw data
mfitrawdata1.m	raw data for frog example 1
mfitgenename.m	gene names for frog examples*)

This code is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the NCI or the individual developers be liable for any claim, damages or other liability of any kind. Use of this code by recipient is at recipient's own risk. NCI makes no representations that the use of the code will not infringe any patent or proprietary rights of third parties.

The source of data is

Yanai, I. Peshkin. L, Jorgenson, P. and Krischner, M.W. (2011) Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility.Developmental Cell, 20(4), 483-496. PMID: 21497761.

Last updated: February 17, 2012