Re: [genesets] GSEA analysis can not display snapshot

[Anthony Castanza]

Hello,

 

This is the address to submit gene sets for consideration for inclusion in MSigDB. Please direct future support requests to the GSEA Help google group: https://groups.google.com/forum/#!forum/gsea-help.

That said, the issue here is that there were one or more infinite, or non-numeric values in GSEA's internal gene ranking used to calculate the enrichment statistic. This normally occurs as a result of divide-by-zeros/near zeros.

How was GSEA run here, in particular what ranking metric was used, and how many samples? In some circumstances the best way to resolve this error is to generate a ranked list outside of GSEA (for example through an unfiltered differential expression analysis), and after ensuring that all values are numeric and finite, running the enrichment analysis though GSEA's preranked mode.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

 

From: 程耀 <cheng...@126.com>
Date: Wednesday, August 4, 2021 at 6:59 PM
To: gene...@broadinstitute.org <gene...@broadinstitute.org>
Subject: [genesets] GSEA analysis can not display snapshot

 

Hi，

  When i run GSEA analysis of my data, the results can not show snapshot. Snapshot of enrichment results as shown below：

 

Trouble saving image

java.lang.IllegalArgumentException: Must be finite. at jfree...@1.5.0/org.jfree.chart.axis.NumberTickUnitSource.getCeilingTickUnit(NumberTickUnitSource.java:114) at jfree...@1.5.0/org.jfree.chart.axis.NumberAxis.selectVerticalAutoTickUnit(NumberAxis.java:896) at jfree...@1.5.0/org.jfree.chart.axis.NumberAxis.selectAutoTickUnit(NumberAxis.java:828) at jfree...@1.5.0/org.jfree.chart.axis.NumberAxis.refreshTicksVertical(NumberAxis.java:1049) at jfree...@1.5.0/org.jfree.chart.axis.NumberAxis.refreshTicks(NumberAxis.java:929) at jfree...@1.5.0/org.jfree.chart.axis.ValueAxis.reserveSpace(ValueAxis.java:806) at jfree...@1.5.0/org.jfree.chart.plot.XYPlot.calculateRangeAxisSpace(XYPlot.java:3077) at jfree...@1.5.0/org.jfree.chart.plot.CombinedDomainXYPlot.calculateAxisSpace(CombinedDomainXYPlot.java:447) at jfree...@1.5.0/org.jfree.chart.plot.CombinedDomainXYPlot.draw(CombinedDomainXYPlot.java:482) at jfree...@1.5.0/org.jfree.chart.JFreeChart.draw(JFreeChart.java:1286) at jfree...@1.5.0/org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1453) at jfree...@1.5.0/org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1434) at jfree...@1.5.0/org.jfree.chart.ChartUtils.writeChartAsPNG(ChartUtils.java:184) at jfree...@1.5.0/org.jfree.chart.ChartUtils.saveChartAsPNG(ChartUtils.java:310) at jfree...@1.5.0/org.jfree.chart.ChartUtils.saveChartAsPNG(ChartUtils.java:285) at org.gsea_msigdb.gsea/edu.mit.broad.genome.charts.XChartImpl.saveAsPNG(XChartImpl.java:114) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.api.PicFile.save(PicFile.java:149) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.api.PicFile.createIMG(PicFile.java:118) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.pages.HtmlPage.addChart(HtmlPage.java:206) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.pages.HtmlPage.addChart(HtmlPage.java:213) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.EnrichmentReports.createReport(EnrichmentReports.java:785) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.EnrichmentReports.createReport(EnrichmentReports.java:613) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.EnrichmentReports.createGseaLikeReport(EnrichmentReports.java:330) at org.gsea_msigdb.gsea/edu.mit.broad.genome.reports.EnrichmentReports.createGseaLikeReport(EnrichmentReports.java:179) at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:124) at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:165) at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:435) at java.base/java.lang.Thread.run(Unknown Source)

 

operating system and version: Mac 11.5.1 (20G80)

GSEA v4.1.0 build 27

java Version 8 Update 301 

 

How can I solve this problem？

 

 

chengyao

 

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