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.

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Andrew Ah Young, Anthony Castanza2

Apr 25

Hi Andrew, The underlying data for everything GSEA produces is written out to the output directory of

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Hi Andrew, The underlying data for everything GSEA produces is written out to the output directory of

Apr 25

Theo, Anthony Castanza3

Apr 24

non human or mouse gsea

Hi Anthony, Thanks for getting back to me. I saw that those conversions exist in the chip file, so I

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non human or mouse gsea

Hi Anthony, Thanks for getting back to me. I saw that those conversions exist in the chip file, so I

Apr 24

Hashan Jayarathne, Anthony Castanza2

Apr 23

Hi Hashan, I'm not sure I follow your question. Are you trying to perform an overlap statistic

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Hi Hashan, I'm not sure I follow your question. Are you trying to perform an overlap statistic

Apr 23

M K, Anthony Castanza3

Apr 19

values of .rnk file in edb folder output

Thanks a lot Antony, Everything is much more clear now. Best regards, mk On Wed, Apr 17, 2024 at 6:42

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values of .rnk file in edb folder output

Thanks a lot Antony, Everything is much more clear now. Best regards, mk On Wed, Apr 17, 2024 at 6:42

Apr 19

Alice Piller, Anthony Castanza5

Apr 19

GSEA for SomaScan assay data

Hi Antony, Thank you for your feedback. I haven't carried out any formal hierarchical clustering.

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GSEA for SomaScan assay data

Hi Antony, Thank you for your feedback. I haven't carried out any formal hierarchical clustering.

Apr 19

Shubin, Anthony Castanza2

Apr 18

Hi Shubin, I replied to the GSEA-Team message you sent, but just for bookkeeping purposes, the issue

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Hi Shubin, I replied to the GSEA-Team message you sent, but just for bookkeeping purposes, the issue

Apr 18

Andrew Young, Anthony Castanza4

Apr 16

Input file error

Hi Andrew, There was a small issue with the header, it had float (decimal) values for the numbers of

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Input file error

Hi Andrew, There was a small issue with the header, it had float (decimal) values for the numbers of

Apr 16

Anthony Castanza

Apr 15

Re: [gsea-help] Analysis of the gsea plot

Hi Sam, GSEA can not be run with just 16 genes, it will not give reasonable results. GSEA is intended

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Re: [gsea-help] Analysis of the gsea plot

Hi Sam, GSEA can not be run with just 16 genes, it will not give reasonable results. GSEA is intended

Apr 15

Justin Blaize, Anthony Castanza5

Apr 12

Chip file issues

These suggestions worked! Thank you so much for your help! On Fri, Apr 12, 2024 at 4:06 PM Anthony

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Chip file issues

These suggestions worked! Thank you so much for your help! On Fri, Apr 12, 2024 at 4:06 PM Anthony

Apr 12

Gordon Zheng, Anthony Castanza2

Apr 12

There are ties in the preranked stats (3.06% of the list).

Hi Gordon. Unfortunately fgsea is a 3rd party reimplementation of the GSEA algorithm (with some

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There are ties in the preranked stats (3.06% of the list).

Hi Gordon. Unfortunately fgsea is a 3rd party reimplementation of the GSEA algorithm (with some

Apr 12

Yu-Hui Lin, Anthony Castanza2

Apr 11

Error using Human Clariom_D v7.5.1 chip

Hello, The error here and the warning are likely unrelated, the warning is standard when GSEA detects

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Error using Human Clariom_D v7.5.1 chip

Hello, The error here and the warning are likely unrelated, the warning is standard when GSEA detects

Apr 11

NAKIM, Anthony Castanza2

Apr 9

GSEA 1006 Error

Hi Nakim, The latest version of GSEA has had numerous bugfixes since version 4.1.0, including to an

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GSEA 1006 Error

Hi Nakim, The latest version of GSEA has had numerous bugfixes since version 4.1.0, including to an

Apr 9

Thammachanok Boonto, Anthony Castanza2

Apr 8

Encounter genes with 0 "RANK METRIC SCORE"

Hi Thammachano, Generally we would recommend filtering out these genes that aren't expressed

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Encounter genes with 0 "RANK METRIC SCORE"

Hi Thammachano, Generally we would recommend filtering out these genes that aren't expressed

Apr 8

Emily Diaz, Helga Thorvaldsdottir10

Apr 8

GSEA v4.3.3 Mac App immediately crashing

Finally got it!! I really appreciate all the advice and guidance Helga!! On Monday, April 8, 2024 at

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GSEA v4.3.3 Mac App immediately crashing

Finally got it!! I really appreciate all the advice and guidance Helga!! On Monday, April 8, 2024 at

Apr 8

Apr 5

post vs pre. -> 1 pathway vs 20 pathways ratio

In the results of a Gene Set Enrichment Analysis (GSEA), comparing 'post' (10 samples) and

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post vs pre. -> 1 pathway vs 20 pathways ratio

In the results of a Gene Set Enrichment Analysis (GSEA), comparing 'post' (10 samples) and

Apr 5

SamSam, Anthony Castanza4

Mar 29

ssGSEA across analysis for multiple dataset

Hi Meg, ssGSEA by itself doesn't use permutations, as it doesn't generate any statistics

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ssGSEA across analysis for multiple dataset

Hi Meg, ssGSEA by itself doesn't use permutations, as it doesn't generate any statistics

Mar 29

Reo, Anthony Castanza3

Mar 29

parsing trouble java.lang.numberformatexception

Hi Léa, Sorry for the delay getting back to you here, for some reason your message got stuck in the

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parsing trouble java.lang.numberformatexception

Hi Léa, Sorry for the delay getting back to you here, for some reason your message got stuck in the

Mar 29

Pumla Bhekiwe MANYATSI, Anthony Castanza3

Mar 29

Should I run the software

Hi Pumla, Based on what I can see of the error message at the bottom of the screenshot it appears

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Should I run the software

Hi Pumla, Based on what I can see of the error message at the bottom of the screenshot it appears

Mar 29

Zehan Song, Anthony Castanza2

Mar 28

different results between GSEA and GSEApy

Hi Zehan, The GSEA desktop application is the only official distribution of GSEA. The GSEApy package

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different results between GSEA and GSEApy

Hi Zehan, The GSEA desktop application is the only official distribution of GSEA. The GSEApy package

Mar 28

Marte Karen Brattås, Anthony Castanza3

Mar 26

Permutation type

Hi Marte, In order to get GSEA to actually use the chip you provide you have to use "Collapse

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Permutation type

Hi Marte, In order to get GSEA to actually use the chip you provide you have to use "Collapse

Mar 26

杨洋, Anthony Castanza2

Mar 26

Problem in setting my acetylation-related gene set

Hello, I'm not able to access the manuscript you linked in order to see precisely what they did (

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Problem in setting my acetylation-related gene set

Hello, I'm not able to access the manuscript you linked in order to see precisely what they did (

Mar 26

Anthony Castanza

Mar 25

Re: [gsea-help] Gene set and chip file for non-standard GSEA application

Hello, I took a look at the data you sent, and at the paper you're referencing and I'm not

unread,

Re: [gsea-help] Gene set and chip file for non-standard GSEA application

Hello, I took a look at the data you sent, and at the paper you're referencing and I'm not

Mar 25

Jeevankumar Ramaswamy Durai, David Eby2

Mar 23

SEP blocking download

Hi Jeevan, Is this on downloading GSEA or on trying to install/run the software? Are you getting a

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SEP blocking download

Hi Jeevan, Is this on downloading GSEA or on trying to install/run the software? Are you getting a

Mar 23

Anu Shivalikanjli, Anthony Castanza2

Mar 21

Expression dataset not loading

Hello, It's difficult to diagnose what might be going wrong here. The file field will only

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Expression dataset not loading

Hello, It's difficult to diagnose what might be going wrong here. The file field will only

Mar 21

Maéva Brunet, Anthony Castanza4

Mar 19

Error1001 in PreRanked protocol

Hi Maéva, If you're having this error occur with even one gene then there's likely some other

unread,

Error1001 in PreRanked protocol

Hi Maéva, If you're having this error occur with even one gene then there's likely some other

Mar 19

enot, Anthony Castanza13

Mar 19

edgeR::voom weighted log2cpm - Most appropriate use of GSEA

Hi Eleni, The only thing you can really do here is to run an increased number of permutations if you

unread,

edgeR::voom weighted log2cpm - Most appropriate use of GSEA

Hi Eleni, The only thing you can really do here is to run an increased number of permutations if you

Mar 19

Salomé CECCARELLI, … Anthony Castanza15

Mar 18

Java error when loading txt file to GSEA

Hi Gavin, Could you try replacing the dashes ("-") in your filename with underscores (

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Java error when loading txt file to GSEA

Hi Gavin, Could you try replacing the dashes ("-") in your filename with underscores (

Mar 18

Nathalie Sippel, Anthony Castanza5

Mar 15

Hi Anthony, Oh I see where the problem is :) Do you have any suggestion on how I can perform

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Hi Anthony, Oh I see where the problem is :) Do you have any suggestion on how I can perform

Mar 15

Vicki Wang, Anthony Castanza4

Mar 12

Mouse strains for mouse gene sets

Hi Vicki, Yeah the gene IDs you have here definitely present a significant difficulty for performing

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Mouse strains for mouse gene sets

Hi Vicki, Yeah the gene IDs you have here definitely present a significant difficulty for performing

Mar 12

Edoardo “Dado” Marcora, Anthony Castanza3

Mar 8

MSigDB GMT files with Ensembl gene ids instead of Entrez IDs or Symbols

Thanks for the clarification. Even though Gene Symbols may provide the most informative output for

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MSigDB GMT files with Ensembl gene ids instead of Entrez IDs or Symbols

Thanks for the clarification. Even though Gene Symbols may provide the most informative output for

Mar 8

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