q-value dependent "Invalid range error" when creating network view

[cviner]

OS: CentOS 6.5 (Linux 2.6.32-431.17.el6.x86_64)
Cytoscape version: 3.2.0
Enrichment Map Plugin version: 2.1.0 Beta 1 Build 619

Building of enrichment maps occasionally (input dependent, as described below) fails at the "creating network view" state with the error: "Invalid range properties".

Tests were conducted with GREAT (version 2.0.2) data, using only a single dataset, no GMT nor expression files, and following the instructions provided at the Enrichment Map GREAT Tutorial, except when otherwise indicated.

This error appears to occur depending upon the value of the FDR (q-value) for a statistical test (likely with respect to the threshold). For example, if either the BinomFdrQ or HyperFdrQ columns is greater than the threshold (0.05), and "BOTH" are selected at the filtering dialogue, then the error often occurs. If only one is <= 0.05, and a statistical test is selected such that its corresponding q-value is below the threshold, often no error occurs.

I provide below some minimal input TSV data to reproduce this error (in order to simplify the test cases, all below tests only filtered based upon the hypergeometric test).

For all of the below examples, the header of the input files was:

# GREAT version 2.0.2   Species assembly: mm9   Association rule: Basal+extension: 5000 bp upstream, 1000 bp downstream, 1000000 bp max extension, curated regulatory domains included
# Ontology summary statistics are provided in the footer.
#
# Ontology  ID  Desc    BinomRank   BinomP  BinomBonfP  BinomFdrQ   RegionFoldEnrich    ExpRegions  ObsRegions  GenomeFrac  SetCov  HyperRank   HyperP  HyperBonfP  HyperFdrQ   GeneFoldEnrich  ExpGenes    ObsGenes    TotalGenes  GeneSetCov  TermCov Regions Genes

Example 1 (error occurs):

GO Molecular Function   GO:0004725  protein tyrosine phosphatase activity   21.052671e-4    3.425391e-1 1.712696e-1 2.991119e+1 1.002969e-1 31.253712e-2    3.750000e-1 8   1.040817e-3 1.000000e+0 4.233523e-1 4.085051e+1 4.895900e-2 2   99  2.000000e-1 2.020202e-2 unnamed,unnamed,unnamed Ptpn13,Ptprc
GO Molecular Function   GO:0008553  hydrogen-exporting ATPase activity, phosphorylative mechanism   1   4.507514e-6 1.466745e-2 1.466745e-2 6.225893e+2 3.212390e-3 2   4.015488e-4 2.500000e-1 13  4.935459e-3 1.000000e+0 1.000000e+0 2.022100e+2 4.945354e-3 110 1.000000e-1 1.000000e-1 unnamed,unnamed Atp6v1g3

Example 2 (swap above two lines; error still occurs):

GO Molecular Function   GO:0008553  hydrogen-exporting ATPase activity, phosphorylative mechanism   1   4.507514e-6 1.466745e-2 1.466745e-2 6.225893e+2 3.212390e-3 2   4.015488e-4 2.500000e-1 13  4.935459e-3 1.000000e+0 1.000000e+0 2.022100e+2 4.945354e-3 110 1.000000e-1 1.000000e-1 unnamed,unnamed Atp6v1g3
GO Molecular Function   GO:0004725  protein tyrosine phosphatase activity   21.052671e-4    3.425391e-1 1.712696e-1 2.991119e+1 1.002969e-1 31.253712e-2    3.750000e-1 8   1.040817e-3 1.000000e+0 4.233523e-1 4.085051e+1 4.895900e-2 2   99  2.000000e-1 2.020202e-2 unnamed,unnamed,unnamed Ptpn13,Ptprc

Example 3 (change HyperFdrQ of first entry to 0.06; error still occurs):

GO Molecular Function   GO:0008553  hydrogen-exporting ATPase activity, phosphorylative mechanism   1   4.507514e-6 1.466745e-2 1.466745e-2 6.225893e+2 3.212390e-3 2   4.015488e-4 2.500000e-1 13  4.935459e-3 1.000000e+0 0.06    2.022100e+2 4.945354e-3 1   10  1.000000e-1 1.000000e-1 unnamed,unnamed Atp6v1g3
GO Molecular Function   GO:0004725  protein tyrosine phosphatase activity   21.052671e-4    3.425391e-1 1.712696e-1 2.991119e+1 1.002969e-1 31.253712e-2    3.750000e-1 8   1.040817e-3 1.000000e+0 4.233523e-1 4.085051e+1 4.895900e-2 2   99  2.000000e-1 2.020202e-2 unnamed,unnamed,unnamed Ptpn13,Ptprc

Example 4 (change HyperFdrQ of first entry to 0.05; error does not occur and the resulting network contains a single node):

GO Molecular Function   GO:0008553  hydrogen-exporting ATPase activity, phosphorylative mechanism   1   4.507514e-6 1.466745e-2 1.466745e-2 6.225893e+2 3.212390e-3 2   4.015488e-4 2.500000e-1 13  4.935459e-3 1.000000e+0 0.05    2.022100e+2 4.945354e-3 1   10  1.000000e-1 1.000000e-1 unnamed,unnamed Atp6v1g3
GO Molecular Function   GO:0004725  protein tyrosine phosphatase activity   21.052671e-4    3.425391e-1 1.712696e-1 2.991119e+1 1.002969e-1 31.253712e-2    3.750000e-1 8   1.040817e-3 1.000000e+0 4.233523e-1 4.085051e+1 4.895900e-2 2   99  2.000000e-1 2.020202e-2 unnamed,unnamed,unnamed Ptpn13,Ptprc

Example 5 (use only the first entry and do not change the output; error does not occur and the resulting network is empty):

GO Molecular Function   GO:0008553  hydrogen-exporting ATPase activity, phosphorylative mechanism   1   4.507514e-6 1.466745e-2 1.466745e-2 6.225893e+2 3.212390e-3 2   4.015488e-4 2.500000e-1 13  4.935459e-3 1.000000e+0 0.05    2.022100e+2 4.945354e-3 1   10  1.000000e-1 1.000000e-1 unnamed,unnamed Atp6v1g3

[risserlin]

fixed in commit 7c75d9f
Available in development release on baderlab website - http://baderlab.org/Software/EnrichmentMap#Development_Versions