gsea-help

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Welcome to the gsea-help group. This is the official help and discussion forum for Gene Set Enrichment (GSEA) and Molecular Signature Database (MSigDB). Please post questions, bug reports, and suggestions here. If you're having a problem, try searching this list to see if your question has already been addressed. If a suggested solution does not address your issue, please create a new topic. Everyone is encouraged to contribute by suggesting bug fixes, and joining discussions of feature enhancements.

Other resources include:

GSEA / MSigDB web site: www.gsea-msigdb.org.

For scientific questions about the GSEA method, review our 2005 GSEA PNAS paper and 2003 Nature Genetics paper.

For questions about using the software and resolving errors, you may find answers in our FAQ, User Guide, or Documentation Wiki.

For questions about terms of use, see the GSEA and MSigDB license page.

For help with errors in GSEA when accessing CHIP annotation files from the Broad website, please see our FAQ.

Due to changes in our annotation process Clariom Array support CHIP files have been moved to: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations_legacy/ These legacy annotations target the specified version of MSigDB, but are constructed using a old to new symbol remapping procedure rather than directly from deposited probe-set level annotations.

If you contact us about a problem with the GSEA desktop application, please send us the following information:

The version of GSEA you are using, your computer operating system, and your version of Java.
The text of any error messages, and the log from the GSEA session that caused the error. To retrieve the log, click the [+] icon in the bottom left of the GSEA window and copy the text.
Optionally, example data that demonstrates the problem.

If you do not wish to create a Google account, please note that you can also sign up by sending an email to gsea-help+subscribe@googlegroups.com with "subscribe" as the subject, and that when signing up you can set your account to avoid receiving emails.

0 selected

Bing-Jian Feng, Anthony Castanza2

May 25

what is this gene set?

Hello, That gene set is part of the CGN subcollection which were all generated as part of the same

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what is this gene set?

Hello, That gene set is part of the CGN subcollection which were all generated as part of the same

May 25

Nicola Chiarelli, Anthony Castanza3

May 24

How to create an .rnk file

Hi Anthony, thanks for the quick response. GSEA using WebGestalt toolkit gives the following error:

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How to create an .rnk file

Hi Anthony, thanks for the quick response. GSEA using WebGestalt toolkit gives the following error:

May 24

Federico Pietrocola, Anthony Castanza3

May 23

Pre-ranked GSEA Error "Specified path is a Directory (expecting a File)"

Problem solved! Thank you, Anthony! -- Federico Pietrocola, Ph.D Karolinska Institute Department of

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Pre-ranked GSEA Error "Specified path is a Directory (expecting a File)"

Problem solved! Thank you, Anthony! -- Federico Pietrocola, Ph.D Karolinska Institute Department of

May 23

Jack McNamara, Anthony Castanza3

May 23

Question regarding input

Great, thank you very much! Jack McNamara Robert Wood Johnson Medical School 2LT, United States Army,

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Question regarding input

Great, thank you very much! Jack McNamara Robert Wood Johnson Medical School 2LT, United States Army,

May 23

Sarah P, Anthony Castanza2

May 20

Hi Sarah, In the screenshot it appears you have the “Collapse/Remap to Gene Symbols” parameter set to

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Hi Sarah, In the screenshot it appears you have the “Collapse/Remap to Gene Symbols” parameter set to

May 20

Eli Kopel, Anthony Castanza3

May 19

Get number of pathways

Thank you very much, Anthony On Thu, May 12, 2022 at 9:21 PM Anthony Castanza <acastanza@cloud.

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Get number of pathways

Thank you very much, Anthony On Thu, May 12, 2022 at 9:21 PM Anthony Castanza <acastanza@cloud.

May 19

Pratibha Garg, Anthony Castanza2

May 17

Unsuccessful run

Hello, Are you using the current release of MSigDB - v7.5.1? There was an error in the preparation of

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Unsuccessful run

Hello, Are you using the current release of MSigDB - v7.5.1? There was an error in the preparation of

May 17

May 17

How to upload new genesets?

Dear GSEA team, I am the head of the Childhood Liver Oncology group at Germans Trias i Pujol Research

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How to upload new genesets?

Dear GSEA team, I am the head of the Childhood Liver Oncology group at Germans Trias i Pujol Research

May 17

zhiheng he, Anthony Castanza2

May 15

Image resolution

Hello, GSEA doesn't have an option to increase the resolution of the default images directly,

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Image resolution

Hello, GSEA doesn't have an option to increase the resolution of the default images directly,

May 15

Kate Park, Anthony Castanza2

May 13

Result interpretation

Hi Kate, Apologies for the delay in getting back to you, we had some discussion internally on the

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Result interpretation

Hi Kate, Apologies for the delay in getting back to you, we had some discussion internally on the

May 13

Josh Spin, Anthony Castanza2

May 9

AFFY Chip annotation mismatch

Hi Josh, It appears that this is data that was quantified at the individual transcript level. GSEA

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AFFY Chip annotation mismatch

Hi Josh, It appears that this is data that was quantified at the individual transcript level. GSEA

May 9

shamima, Anthony Castanza2

May 9

Heatmaps missing

Hi Shamima, I'm not exactly sure what you're asking about. What do you mean by you used

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Heatmaps missing

Hi Shamima, I'm not exactly sure what you're asking about. What do you mean by you used

May 9

Ak, Anthony Castanza3

May 5

Question about "List L" in PNAS paper 2005

Hi Anthony, Thank you for your response and the great information! Sincerely, Ak 2022年5月5日木曜日 1:26:58

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Question about "List L" in PNAS paper 2005

Hi Anthony, Thank you for your response and the great information! Sincerely, Ak 2022年5月5日木曜日 1:26:58

May 5

Luca Sigalotti, Anthony Castanza2

May 3

duplicate gene name in pre-ranked GSEA

Hi Luca, If you used GSEA's built in Collapse/Remap dataset function with the "Remap_only

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duplicate gene name in pre-ranked GSEA

Hi Luca, If you used GSEA's built in Collapse/Remap dataset function with the "Remap_only

May 3

Xianjun Dong, Anthony Castanza4

May 2

Incomplete GO terms

Hi Xianjun, This information is supposed to be stored under the "filteredBySimilarity" key

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Incomplete GO terms

Hi Xianjun, This information is supposed to be stored under the "filteredBySimilarity" key

May 2

Ramon Garcia Areas, … David Eby31

May 2

First time GSEA

Hi Ramón, This is a relatively new error message added with GSEA 4.2.0 but the meaning is pretty

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First time GSEA

Hi Ramón, This is a relatively new error message added with GSEA 4.2.0 but the meaning is pretty

May 2

Roni Haas, Anthony Castanza5

Apr 29

The effect direction of genes in the Hallmark Cancer Pathways

Thank you very much for confirming! Best, Roni On Friday, April 29, 2022 at 9:56:08 AM UTC-7 Anthony

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The effect direction of genes in the Hallmark Cancer Pathways

Thank you very much for confirming! Best, Roni On Friday, April 29, 2022 at 9:56:08 AM UTC-7 Anthony

Apr 29

Hicham Hboub, Anthony Castanza6

Apr 28

GSEA analysis for one gene against datasets of another one

GSEA is gene set enrichment analysis. It looks of the enrichment of a set of genes in a ranked list

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GSEA analysis for one gene against datasets of another one

GSEA is gene set enrichment analysis. It looks of the enrichment of a set of genes in a ranked list

Apr 28

Sarah Rashid, Anthony Castanza9

Apr 27

GSEA analysis plots

Hi Anthony, Thanks for your response. I am using C2 Kegg (curated) for pathway analysis.

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GSEA analysis plots

Hi Anthony, Thanks for your response. I am using C2 Kegg (curated) for pathway analysis.

Apr 27

shamima, Anthony Castanza10

Apr 25

Can't upload the input file in GSEA-Preranked

Hello, If the file isn't showing up in the dropdown, it likely has an incorrect file extension.

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Can't upload the input file in GSEA-Preranked

Hello, If the file isn't showing up in the dropdown, it likely has an incorrect file extension.

Apr 25

Sarah P, Anthony Castanza2

Apr 25

GSEA analysis using DEG

Hi Sarah, A study similar to this was, in fact, one of the foundational studies for the GSEA

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GSEA analysis using DEG

Hi Sarah, A study similar to this was, in fact, one of the foundational studies for the GSEA

Apr 25

Nicholas Sing, Anthony Castanza2

Apr 22

Output the Enrichment Results .tsv File Only

Hi Nicholas, GSEA includes TSV's for all the outputs in the results directory for each job run,

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Output the Enrichment Results .tsv File Only

Hi Nicholas, GSEA includes TSV's for all the outputs in the results directory for each job run,

Apr 22

Yuliang Wang, David Eby3

Apr 20

Request for GSEA 4.1.2

well thank you David Eby <eby@broadinstitute.org> 于2022年4月20日周三 00:19写道： Hi, I have followed up

unread,

Request for GSEA 4.1.2

well thank you David Eby <eby@broadinstitute.org> 于2022年4月20日周三 00:19写道： Hi, I have followed up

Apr 20

Sarah Philippi, Anthony Castanza16

Apr 20

Questions for Running GSEA using Proteomics Data

Hi Anthony, Thank you for the information, it's very appreciated! On Monday, April 18, 2022 at 12

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Questions for Running GSEA using Proteomics Data

Hi Anthony, Thank you for the information, it's very appreciated! On Monday, April 18, 2022 at 12

Apr 20

Jack McNamara, Anthony Castanza2

Apr 13

Converting Ensembl Transcript IDs to Gene IDs

Hi Jack, From the GEO accession pages for the individual samples, it looks like this data was

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Converting Ensembl Transcript IDs to Gene IDs

Hi Jack, From the GEO accession pages for the individual samples, it looks like this data was

Apr 13

Gautam Nisha, Anthony Castanza37

Apr 8

Regarding RNA SEQ data as RPKM values

Ok, I didn't realize this was the same data you'd run before, my answer assumed it was a

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Regarding RNA SEQ data as RPKM values

Ok, I didn't realize this was the same data you'd run before, my answer assumed it was a

Apr 8

Candice Contet, Anthony Castanza3

Apr 7

background set and ranking metrics

Hi Anthony, thanks for clarifying the issue of background set. This scenario is what I was hoping for

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background set and ranking metrics

Hi Anthony, thanks for clarifying the issue of background set. This scenario is what I was hoping for

Apr 7

Kevin Lee, David Eby2

Apr 5

GSEA ghost files on Windows

Hi Kevin, Yes, you are correct. I wouldn't say it's "intended" behavior, but GSEA

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GSEA ghost files on Windows

Hi Kevin, Yes, you are correct. I wouldn't say it's "intended" behavior, but GSEA

Apr 5

Maria Villa, Anthony Castanza3

Apr 4

Samples belonging to continuous labels

Hello, Anthony, Thank you very much, that makes perfect sense. Best regards, Maria. El jueves, 31 de

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Samples belonging to continuous labels

Hello, Anthony, Thank you very much, that makes perfect sense. Best regards, Maria. El jueves, 31 de

Apr 4

Zhenyu Zhang, Anthony Castanza2

Apr 1

MSigDB version for Ensembl102

Hello, Unfortunately we're only able to produce an MSigDB version in sync with ever other Ensembl

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MSigDB version for Ensembl102

Hello, Unfortunately we're only able to produce an MSigDB version in sync with ever other Ensembl

Apr 1

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