Two Species Clustering - Parameter Specification

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dataFile_hm= microarray expression data for species I

dataFile_ms= microarray expression data for species II

k = cluster number

scatter_num = 0 (default)

annotFile_hm = annotation file for species I

annotFile_ms = annotation file for species II

orthologFile = Ortholog file of probes to probes across species

kmeans_result_hm = (default, no use)

kmeans_result_ms = (default, no use)

outputFile_hm = output file containing the clustering results of species I

outputFile_ms = output file containing the clustering results of species II

k_by_k_output_clusters = output file containing the combined clustering results for the two species

outputFile_diag_hm = (default, no use)

outputFile_diag_ms = (default, no use)

gene_pair_result = output file containing the information of each ortholog pair and its cluster index

prep = yes: to perform preprocess; no: not to do the preproces

CVThr = (0-100) all genes whose coefficient of variance is less than this value will be filtered out

maxExpr = (50-200) all genes whose maximum expression level is less than this value will be filtered out

regulatorCVThr = 0 (default)

regulatorMaxExpr = 0 (default)

regulatorGenesFile = (default)

C:\juncai\workshop\TwoSpeciesClustering\realdata\aging\human&fly\emptylist.txt

KmeanMaxIter = 1 (default)

MaxIterNum = 1 (default)

nMaxAlgRun = (1-150) (randomly repetitive running times)

stoppingThr = (0.001-0.00001 the threshold used in assessing stopping criteria - if the relative increase of score in iteration is less than this value, the algorithm will stop

psudo_uniform_counts = psudo counts added to scatter prior, 0: no scatter cluster; >=1(integer) the scatter cluster exits.

Result_File_Dep = (default, no use)

Kmeans_Converge_Result = (default, no use)