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. 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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Priyanka Manandhar, Anthony Castanza2

Sep 17

generating GSEA analysis from a particular dataset

Hi Priya, I'm not entirely sure what you mean by a "single targeted dataset" do you

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generating GSEA analysis from a particular dataset

Hi Priya, I'm not entirely sure what you mean by a "single targeted dataset" do you

Sep 17

Anthony Castanza

Sep 15

Re: [gsea-help] phenotype continuous

Hi Tabita, This error is caused by the ranking metric selected for the dataset being incompatible

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Re: [gsea-help] phenotype continuous

Hi Tabita, This error is caused by the ranking metric selected for the dataset being incompatible

Sep 15

Dong, Anthony Castanza6

Sep 14

help on Ensemble ID to Gene Symbol conversion

I performed these remappings using data from our chip files for NCBI/Entrez Gene IDs, Ensembl Gene

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help on Ensemble ID to Gene Symbol conversion

I performed these remappings using data from our chip files for NCBI/Entrez Gene IDs, Ensembl Gene

Sep 14

Dong, Anthony Castanza8

Sep 14

Continuous variable for GSEA analysis

I just tried increasing the permutation number to 10K and ran GSEA against the customized collection

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Continuous variable for GSEA analysis

I just tried increasing the permutation number to 10K and ran GSEA against the customized collection

Sep 14

Helena Izquierdo, Anthony Castanza6

Sep 14

Error at loading gene dataset

Hi Helena, I downloaded the xlsm file you'd attached to your message, opened it in Excel, File

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Error at loading gene dataset

Hi Helena, I downloaded the xlsm file you'd attached to your message, opened it in Excel, File

Sep 14

Elizabeth Bartom, … Anthony Castanza12

Sep 14

After pruning, none of the gene sets passed size thresholds

When using the annotate page to perform an overlap statistic test, GSEA internally uses the

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After pruning, none of the gene sets passed size thresholds

When using the annotate page to perform an overlap statistic test, GSEA internally uses the

Sep 14

Dong, Anthony Castanza7

Sep 14

how to interpret enrichment plot

Hi Anthony, I have one more question related to analysis using continuous variable. As suggested by

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how to interpret enrichment plot

Hi Anthony, I have one more question related to analysis using continuous variable. As suggested by

Sep 14

Ramon GA, Anthony Castanza2

Sep 13

Waterfall plots

Hi Ramón, Unfortunately no, the visualizations you see on the website are all we offer in terms of

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Waterfall plots

Hi Ramón, Unfortunately no, the visualizations you see on the website are all we offer in terms of

Sep 13

samy amin, Anthony Castanza2

Sep 13

GSEA input file DEG genes

Hi Samy, If you have the full list and not just (for example) the significant genes, you can format

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GSEA input file DEG genes

Hi Samy, If you have the full list and not just (for example) the significant genes, you can format

Sep 13

Luca Sigalotti, … Anthony Castanza5

Sep 12

GSEA preranked with signed -log10 p value

The GSEA website only performs a simple hypergeometric "overlap statistic" test. The full

unread,

GSEA preranked with signed -log10 p value

The GSEA website only performs a simple hypergeometric "overlap statistic" test. The full

Sep 12

Dong, Anthony Castanza5

Sep 12

How to get enrichment plot in SVG format that is located at around 1000th position?

Hi Anthony, Thank you so much! Dong On Sunday, September 12, 2021 at 4:36:46 PM UTC-4 Anthony

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How to get enrichment plot in SVG format that is located at around 1000th position?

Hi Anthony, Thank you so much! Dong On Sunday, September 12, 2021 at 4:36:46 PM UTC-4 Anthony

Sep 12

Dong, Anthony Castanza3

Sep 12

GSEA analysis against customized collection

I see. Thank you so much! Dong On Sunday, September 12, 2021 at 2:25:19 PM UTC-4 Anthony Castanza

unread,

GSEA analysis against customized collection

I see. Thank you so much! Dong On Sunday, September 12, 2021 at 2:25:19 PM UTC-4 Anthony Castanza

Sep 12

Hexin Chen, Anthony Castanza2

Sep 8

GSEA analysis of RNA-seq data

Hi Hexin, I wasn't able to replicate this error with the two files you sent as input. This error

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GSEA analysis of RNA-seq data

Hi Hexin, I wasn't able to replicate this error with the two files you sent as input. This error

Sep 8

Alex Lorenzo Starr, Anthony Castanza3

Sep 3

GSEA Preranked Assuming gene-gene expression independence

No worries, I figured it was a long shot. Thanks for taking the time! Best, Alex. On Friday,

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GSEA Preranked Assuming gene-gene expression independence

No worries, I figured it was a long shot. Thanks for taking the time! Best, Alex. On Friday,

Sep 3

WANG Zifeng, … Anthony Castanza7

Aug 28

Renaming rpt dir on error

Dear Anthony, I overwrite the old files. So I can't send it to you. I re-run the program again,

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Renaming rpt dir on error

Dear Anthony, I overwrite the old files. So I can't send it to you. I re-run the program again,

Aug 28

Priyanka Manandhar, Anthony Castanza3

Aug 24

That makes perfect sense. Thank you, it worked out.

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That makes perfect sense. Thank you, it worked out.

Aug 24

Joe Horder, Anthony Castanza4

Aug 24

Phenotype permutation vs gene-set permutation

Hi Joe, This is correct. -Anthony Anthony S. Castanza, PhD Curator, Molecular Signatures Database

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Phenotype permutation vs gene-set permutation

Hi Joe, This is correct. -Anthony Anthony S. Castanza, PhD Curator, Molecular Signatures Database

Aug 24

Patrick Tamukong, … Anthony Castanza8

Aug 23

Which Enrichment Statistic should I use for Microarray Data, Which Metric for Ranking genes from log-transformed microarray data?

Thanks very much Anthony. Patrick On Monday, August 23, 2021 at 1:21:53 PM UTC-7 Anthony Castanza

unread,

Which Enrichment Statistic should I use for Microarray Data, Which Metric for Ranking genes from log-transformed microarray data?

Thanks very much Anthony. Patrick On Monday, August 23, 2021 at 1:21:53 PM UTC-7 Anthony Castanza

Aug 23

priyadarshini nambiar, Anthony Castanza3

Aug 23

how to get RNA seq data for GSEA

Thank you, Anthony, Appreciate your help Regards, Priya On Mon, 23 Aug 2021 at 21:28, Anthony

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how to get RNA seq data for GSEA

Thank you, Anthony, Appreciate your help Regards, Priya On Mon, 23 Aug 2021 at 21:28, Anthony

Aug 23

Chris Pam, Anthony Castanza3

Aug 18

Gene Ontology terms and their GO IDs

Hi, Sorry about that, Google Groups wasn't cooperating. Did the attachment come through this time

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Gene Ontology terms and their GO IDs

Hi, Sorry about that, Google Groups wasn't cooperating. Did the attachment come through this time

Aug 18

Mike, … Anthony Castanza5

Aug 13

MSigDB databases for mouse

Cool! Thank you so much for your great help, Anthony! Have a great weekend! Mike On Friday, August 13

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MSigDB databases for mouse

Cool! Thank you so much for your great help, Anthony! Have a great weekend! Mike On Friday, August 13

Aug 13

席甲甲, … Anthony Castanza4

Aug 13

missing NOM p-val

Hi Jiajia, Thanks for sending these plots! 1) The description of the enrichment plots and how to

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missing NOM p-val

Hi Jiajia, Thanks for sending these plots! 1) The description of the enrichment plots and how to

Aug 13

Aushia Tanzih Alhaq, Anthony Castanza3

Aug 13

Clariom D mouse analysis

Hi Anthony, Thanks a lot for your prompt answer. I used the 'Collapse' parameter, but chose

unread,

Clariom D mouse analysis

Hi Anthony, Thanks a lot for your prompt answer. I used the 'Collapse' parameter, but chose

Aug 13

Luís Eduardo Gonçalves, Anthony Castanza2

Aug 13

Transcription Factor Enrichment

Hi Luis, There are two Transcription factor target collections, c3.tft.gtrd.v7.4.symbols.gmt

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Transcription Factor Enrichment

Hi Luis, There are two Transcription factor target collections, c3.tft.gtrd.v7.4.symbols.gmt

Aug 13

Dong, Anthony Castanza3

Aug 10

how to run GSEA analysis on the custom genesets (example is provided)

Hi Anthony, I notice that figure 2a mentioned about ssGSEA. What is the really difference between

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how to run GSEA analysis on the custom genesets (example is provided)

Hi Anthony, I notice that figure 2a mentioned about ssGSEA. What is the really difference between

Aug 10

Jiwoon Park, Anthony Castanza4

Aug 6

Preranked GSEA - pathways that look significant with heatmaps are not significant

The mode of calculating nulls that you're describing is similar to that used in the Phenotype

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Preranked GSEA - pathways that look significant with heatmaps are not significant

The mode of calculating nulls that you're describing is similar to that used in the Phenotype

Aug 6

席甲甲, … Dong12

Aug 6

How to check the detail of gene set out of top 20 sets

Hi Anthony, Thanks for looking into this. So, if I want to manually specify a seed, I need to choose

unread,

How to check the detail of gene set out of top 20 sets

Hi Anthony, Thanks for looking into this. So, if I want to manually specify a seed, I need to choose

Aug 6

Anthony Castanza

Aug 5

Re: [genesets] GSEA analysis can not display snapshot

Hello, This is the address to submit gene sets for consideration for inclusion in MSigDB. Please

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Re: [genesets] GSEA analysis can not display snapshot

Hello, This is the address to submit gene sets for consideration for inclusion in MSigDB. Please

Aug 5

zhiheng he, Anthony Castanza5

Aug 4

matrix's fColCnt:6

Hello, I have sent my data to gsea-team@broadinstitute.org. Maybe it is not a usual mail for you. 在

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matrix's fColCnt:6

Hello, I have sent my data to gsea-team@broadinstitute.org. Maybe it is not a usual mail for you. 在

Aug 4

Elena Borroni, Anthony Castanza2

Aug 4

beta-arrestins signature

Hi Elena, For your specific proteomic workflow, you probably want something more like this: https://

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beta-arrestins signature

Hi Elena, For your specific proteomic workflow, you probably want something more like this: https://

Aug 4

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