What this message means? thanks

[Rumela Chakrabarti]

---- Full Error Message ----
After pruning, none of the gene sets passed size thresholds.

---- Stack Trace ----
# of exceptions: 1
------After pruning, none of the gene sets passed size thresholds.------
xtools.api.param.BadParamException: After pruning, none of the gene sets passed size thresholds.
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.gsea.GeneSetCohort$Generator.checkForZeroContentGeneSets(GeneSetCohort.java:227)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.gsea.GeneSetCohort$Generator.filterGeneSetsByMembersAndSize(GeneSetCohort.java:201)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:97)
at org.gsea_msigdb.gsea/xtools.gsea.GseaPreranked.execute_one(GseaPreranked.java:142)
at org.gsea_msigdb.gsea/xtools.gsea.GseaPreranked.execute(GseaPreranked.java:99)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)

--

 

 

Rumela Chakrabarti, PhD

Associate Professor, Tumor Biology Program

Sylvester Comprehensive Cancer Center

Co-Director of Surgical Breast Cancer Research Group

Department of Surgery, Miller School of Medicine

Room 508, Biomedical Research Building 

1501 NW 10^th Avenue, 5^th Floor

Miami, FL 33136

Office phone: 305-243-6545

Cell:3303891943

[Anthony Castanza]

Hi Rumela,

This error means that GSEA failed to analyze the dataset because when it attempted to score the gene sets of interest none of them had a minimum of 15 gene identifiers (default parameter) represented in the dataset being analyzed. 

This is essentially a sanity check on the data to ensure that everything is roughly in line with the algorithm's expectations.

The most likely cause is that your dataset was either highly filtered and didn't contain expression data for all expressed genes, or that the gene identifiers in your file didn't match the identifiers used in the gene sets and no (or invalid) collapse parameters were set.

If you send me a screenshot of your Run GSEA window showing the parameters you selected (particularly any chip file you selected), as well as a sampling of the gene identifiers from your input dataset (including screenshot of the top of the file would be best), I should be able to make some suggestions to get the analysis working.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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