GSEA for RNASEQ
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Entering edit mode
6.3 years ago
Ron ★ 1.0k

Hello all,

I have the FPKM values from NORMAL vs TUMOR.I am doing GSEA analysis using GSEA guy.

Below is my input:

NAME DESCRIPTION Tumor Normal
AKR1B10 na 9.19 0.03
RN7SL1 na 10087.1 32.32
SNORA70 na 220.78 0.72
SNORA22 na 42.12 0.14

I have created a gmt format gene-set.When I try to Run GSEA,I get the following error:

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 xtools.api.param.ParamFactory.checkAndBarfIfZeroSets(EIKM)
    at xtools.gsea.Gsea.execute(EIKM)
    at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(EIKM)
    at java.lang.Thread.run(Thread.java:745)

My parameters are:

Phenotype labels: Normal vs Tumor

Chip Platform:GENE_SYMBOL.chip

Has anyone encountered similar Error?

gsea RNA-Seq next-gen gene • 9.3k views
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Entering edit mode
6.3 years ago
kanwarjag ★ 1.1k

As per error you may like to reduce the no of genes threshold from default 20 to 10 or something less.

However, I would suggest using pre-ranked analysis in GSEA for your ranked gene list.

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Entering edit mode
6.3 years ago
Ron ★ 1.0k

My dataset already had gene-symbols,so I made a parameter change in"Collapse to gene symbols" to False ,and it worked.

Basically these errors come up when you need to change some parameters.

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