GSEA help

[Golam Khandakar]

Hello 

I tried to figure out the problem but was unable to do this. Can anyone help me to figure out the problem what mistake did I make? Thanks. Its still showing error. 

[Golam Khandakar]

The error message is as follows

---- Full Error Message ----
The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub ...

---- Stack Trace ----
# of exceptions: 1
------The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_ILLUMINA_Array_MSigDB.v7.3.chip------
xtools.api.param.BadParamException: The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_ILLUMINA_Array_MSigDB.v7.3.chip
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.getDataset(Gsea.java:109)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:164)
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)

[Golam Khandakar]

---- Full Error Message ----
The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub ...

---- Stack Trace ----
# of exceptions: 1
------The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_ILLUMINA_Array_MSigDB.v7.3.chip------
xtools.api.param.BadParamException: The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_ILLUMINA_Array_MSigDB.v7.3.chip
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.getDataset(Gsea.java:109)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:164)
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)

On Friday, April 4, 2025 at 5:50:25 PM UTC-4 Golam Khandakar wrote:

[Anthony Castanza]

Hello,

The error message you sent doesn't exactly match the screenshot, so I'm not entirely sure what CHIP file you're trying to use, in the screenshot you've selected the Ensembl Gene ID chip intended for RNA-seq data, but in the quoted error message you've selected the Illumina microarray chip file. I'm going to assume you're doing RNA-sequencing work from an Illumina platform and the selection of the Illumina array chip was a misunderstanding.
For the Ensembl Gene ID chip, your data must be in the format of canonical, unversioned, ensembl IDs, e.g. ENSG0000012345 (human), or ENSMUSG00012345 (mouse), if your data has version suffixes (e.g.  ENSG0000012345.2), you will need to strip the trailing versions.

If this issue continues to occur, you would likely need to provide us some examples of the IDs from your dataset file so that we can determine the proper chip file.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[Golam Khandakar]

Hi Anthony,

Thanks for your help. Right now I can run this without any error message. But one thing I am still confused about is. Can you please let me know which one is correct? When I run the GSEA in the permutation type, which category do I select: phenotype/gene set? As i watched in the tutorial and came to know that if more than 7 samples in each group I have to select the phenotype, but if there are fewer than 7, then gene set. I have total 6 samples and i am. trying to compare control  (3 samples) vs treatment group (3 samples). In that case do i need to select gene-set? I tried with both phenotype and gene set. Both of them provide me success result. So i want to know which one is correct. Looking forward to hearing from you.

Kind Regards

Golam Iftakhar Khandakar,PhD

The Ohio State University wexner Medical Center

[Anthony Castanza]

Hello,

Sorry about the delay in getting back to you on this. When you have a dataset with this few number of samples it is not mathematically possible to create enough unique valid permutations with "phenotype" permutation metric. Gene Set permutation is the correct method here.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[Golam Khandakar]

Thank you. Got it. It works. 

Kind Regards 

GOLAM Iftakhar Khandakar 

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