HClust

Input file in seltag format

List of fields - List of expression fields (tissues) used to calculate correlation between gene expression profiles, namely field indices in data format of input file starting from 1 (column numeration is not depend on the Case Names option). Examples of input:
1;2;3-7;12;
1-12;
Selection data - Filename for fields selection in XML format. This is another way to set the list of fields.

List of genes - List of genes to calculate correlation, namely gene indices in data set of input file starting from 1 (column numeration is not depend on the Case Names option). Examples of input:
1;2;3-7;12;
1-12;
Gene list - Filename for genes selection in XML format for Gene List 1. This is another way to set the list of genes.

Name of output file

Three types of distance are possible with respect to correlation coefficient r_ij: 1-r_ij; 1-|r_ij|; 1+r_ij

Type of correlation coefficient. Three types of correlations are possible: Pearson's r, Spearman rank correlation and Kendall tau correlation.

The value of clustering threshold.

Option to treat missing data. Several options are possible: Substitute by means (missing data are substituted by expression means in corresponding field); Case-wise deletion (correlations/distances are calculated by excluding cases that have missing data for any of the selected variables, all correlations are based on the same set of data); Pair-wise deletion (correlations/distances between each pair of profiles are calculated from all fields/samples having valid data for those two profiles).