GSEA for RNASEQ

Question

[Ron]

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?

Answer 1

[kanwarjag]

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.

[Ron]

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.