SelCorr


Input
SelTag 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;
Fields list - Filename for fields selection in XML format. This is another way to set the list of fields.
Genes for select   Genes for select - 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.
Genes for comparison   Genes for comparison - List of genes to which 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 2. This is another way to set the list of genes.
Output
Result   Name of output file
  Correlation matrix   Output correlation matrix for selected genes
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.
Gene selection file   Selected genes can be additionally saved in XML file to be used further by MQSelTag. This parameter specify the name of the output selection file.
Name   Name of output selection.
Comment   Commentary for the output selection.
Options
Type of correlation Type of correlation coefficient. Three types of correlations are possible: Pearson's r, Spearman rank correlation and Kendall tau correlation.
Selection regime Regime to treat multiple genes to compare with single gene. Several options are possible:
Max. correlation value to select - the maximal correlation value between expression profiles in gene set to query gene is evaluated;
Aver. correlation value to select - average correlation coefficient value is calculated;
Corr. for aver field values to select - mean expression values are calculated in the set of genes and their correlation for the query expression profile is calculated.
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).