File descriptions
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core files:

simulation_study_gg_constant_variance3.txt	simulation study for data generated from the GG model
simulation_study_gg_variable_variance3.txt	simulation study for data generated from the extended GG model
simulation_study_lnn_constant_variance3.txt	simulation study for data generated from the LNN model
simulation_study_lnn_variable_variance3.txt	simulation study for data generated from the extended LNN model
graph_a.txt					plotting graphs for the simulation results

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other files:

gg_pr.R			defining gg.pr() to be called by the core files
elnn.R			defining elnn() to be called by the core files

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Function Definitions:



gg.pr

Description:

     To perform the extended Gamma-Gamma analysis on microarray data.

Usage:

gg.pr <- function(data, pattern, dump=F, dump.a=F, dump.z=F, file="mle_gg_pr.txt", file.a="mle_gg_pr_a.txt", file.z="mle_gg_pr_z.txt", header=null, header2=null)

Arguments:

    data: A matrix.  Each row is for measurements of one gene.  Successive measurements on each row are separated by a space
          character.  The number of measurements stored on each line is equal to the total number of replicates.  The number
	  of replicates for each condition may or may not be equal.

 pattern: A text string indicating to which condition each data item within one line belongs to.  For example, if the data
	  have 3 replicates for condition 1 and 5 for condition 2, and the 3 measurements for condition 1 are stored at
          columns 3, 5 and 6, then pattern should be written as "2 2 1 2 1 1 2 2".

    dump: a logical value indicating whether the estimates obtained from the EM algorithm will be saved as a text file

  dump.a: a logical value indicating whether the estimates of the gene-specific shape parameters (a_G) will be saved as a     	  text file

  dump.z: a logical value indicating whether the estimates of the posterior probability of change will be saved as a text     	  file

  file, file.a, file.z: names of the files to store the estimation results

  header: user-defined headings for file

 header2: user-defined headings for file.a and file.z




elnn

Description:

	To perform the extended Lognormal-Normal analysis on microarray data.

Usage:

elnn <- function(data, pattern, dump=F, dump.z=F, file="mle_elnn.txt", file.z="mle_elnn_z.txt", header=null, header2=null) 

Arguments:

    data: A matrix.  Each row is for measurements of one gene.  Successive measurements on each row are separated by a space
          character.  The number of measurements stored on each line is equal to the total number of replicates.  The number
	  of replicates for each condition may or may not be equal.

 pattern: A text string indicating to which condition each data item within one line belongs to.  For example, if the data
	  have 3 replicates for condition 1 and 5 for condition 2, and the 3 measurements for condition 1 are stored at
          columns 3, 5 and 6, then pattern should be written as "2 2 1 2 1 1 2 2".

    dump: a logical value indicating whether the estimates obtained from the EM algorithm will be saved as a text file

  dump.z: a logical value indicating whether the estimates of the posterior probability of change will be saved as a text               file

  file, file.z: names of the files to store the estimation results

  header: user-defined headings for file

  header2: user-defined headings for file.z