GeneCorr

Input
Expression data   Input file in seltag format
Fields select   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.
Genes for select   List 1 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 1 - Filename for genes selection in XML format for Gene List 1. This is another way to set the list of genes.
Genes for comparison   List 2 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 2 - Filename for genes selection in XML format for Gene List 2. This is another way to set the list of genes.
Output
Result   Name of output file
XML data Name of the file for graphical output of correlation coefficient value profiles. If not specified then no graph output assumed.
Title User-specified title of the graph plot.
Author User-specified name of the graph author.
Comment User-specified graph additional commentary line.
X axis name User-specified graph X axis name.
Y axis name User-specified graph Y axis name.
Options
Type of correlation Type of correlation coefficient. Three types of correlations are possible: Pearson's r, Spearman rank correlation and Kendall tau correlation.
Correlation threshold type Type of threshold to select best correlating gene pairs. Several options are possible: Best N correlations ; Best % correlations; Correlation coefficient value; Select all pairs.
Correlation threshold value Threshold to select genes from List 1 on the basis of the their correlation coefficient value to genes from List 2.
Missing data treatment 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).