GenePattern Help Forum

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Welcome to the GenePattern help forum. This is a place to get help from GenePattern team members and fellow GenePattern users and also a place to post anything you've found useful in using GenePattern.

More information about GenePattern can be found at https://genepattern.org, where you can also sign up to follow us on Facebook and Twitter.

Happy posting!

-The GenePattern team

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10:02 AM

GSEA upload error

Hello! I've been consistently running into an error message when trying to run the GSEA module on

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GSEA upload error

Hello! I've been consistently running into an error message when trying to run the GSEA module on

10:02 AM

vineelaga...@gmail.com

Sep 24

ssGSEA web version run error

Hi I am seeing this error for ssGSEA, with my rpkm expression matrix and geneset.gmt file. I tried

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ssGSEA web version run error

Hi I am seeing this error for ssGSEA, with my rpkm expression matrix and geneset.gmt file. I tried

Sep 24

Sumithra Sankararaman, Barbara Hill2

Sep 24

coverage file not found in MutSigCV

Hello Sumithra, Apologies for the confusion. You can find the file here: https://datasets.genepattern

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coverage file not found in MutSigCV

Hello Sumithra, Apologies for the confusion. You can find the file here: https://datasets.genepattern

Sep 24

Si. Ri., Anthony Castanza2

Sep 21

GSEA with NanoString data

Hello, I'm not exactly sure which blog posts you're referring to but, unless the experiment

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GSEA with NanoString data

Hello, I'm not exactly sure which blog posts you're referring to but, unless the experiment

Sep 21

Arun Jajoriya, Ted Liefeld2

Sep 20

Arun the VennDiagram module is one of our old, deprecated, Java visualizers. You may be able to get

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Arun the VennDiagram module is one of our old, deprecated, Java visualizers. You may be able to get

Sep 20

Shweta Johari, Anthony Castanza4

Sep 7

Text to GCT file

Hello, It looks like your operating system is hiding known file extensions by default. You'll

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Text to GCT file

Hello, It looks like your operating system is hiding known file extensions by default. You'll

Sep 7

Angelussong, Barbara Hill5

Sep 3

Gene Alias Issues in MutSigCV

Hi Barbara, I think I found a fix by mapping all the gene symbols in my datasets to the ones in

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Gene Alias Issues in MutSigCV

Hi Barbara, I think I found a fix by mapping all the gene symbols in my datasets to the ones in

Sep 3

man...@broadinstitute.org, Barbara Hill5

Sep 2

Hello Bobbie, Thanks. I'll try to get it running using the R2.5 container and then get back to

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Hello Bobbie, Thanks. I'll try to get it running using the R2.5 container and then get back to

Sep 2

GenePattern Help Forum

Sep 1

Announcement: Correction: Salmon is now available in GenePattern!

Salmon is now available in GenePattern! Create indices and quantify both bulk and single-cell RNA seq

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Announcement: Correction: Salmon is now available in GenePattern!

Salmon is now available in GenePattern! Create indices and quantify both bulk and single-cell RNA seq

Sep 1

shamaine....@gmail.com, Edwin Juarez4

Aug 25

Nearest Template Prediction

Shamaine, I think the issue is that the module does not actually support 1 sample, despite the

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Nearest Template Prediction

Shamaine, I think the issue is that the module does not actually support 1 sample, despite the

Aug 25

Carlo Donato, … Ted Liefeld12

Aug 12

Unable to Login on GenePattern in the Cloud

Hello Ted, I really appreciate the chance of speaking with you, I just can't tomorrow and Monday

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Unable to Login on GenePattern in the Cloud

Hello Ted, I really appreciate the chance of speaking with you, I just can't tomorrow and Monday

Aug 12

Tongjun Gu, Barbara Hill3

Aug 9

Hello, In both cases your jobs output an error file "ErrorReport" "Your job was

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Hello, In both cases your jobs output an error file "ErrorReport" "Your job was

Aug 9

Tim Chan, Ted Liefeld8

Aug 2

How to setup "Email Reminder"?

Hi I think this would be set in the genepattern.properties file. Look for the keys fqHostName and

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How to setup "Email Reminder"?

Hi I think this would be set in the genepattern.properties file. Look for the keys fqHostName and

Aug 2

Abby X, … qingy...@gmail.com6

Aug 1

File transfer error

Hi, I tried to upload the files to "Files" and drag from there. And it worked. I wonder if

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File transfer error

Hi, I tried to upload the files to "Files" and drag from there. And it worked. I wonder if

Aug 1

GenePattern Help Forum

Jul 29

Announcement: TCGA.SampleSelection has been updated with better error handling

TCGA.SampleSelection has been updated with better error handling for invalid and unmappable genes.

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Announcement: TCGA.SampleSelection has been updated with better error handling

TCGA.SampleSelection has been updated with better error handling for invalid and unmappable genes.

Jul 29

Hui Shinyee, Ted Liefeld5

Jul 28

Hi Ted, Yeah the link to zipped file didn't work as well. I had downloaded the required files

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Hi Ted, Yeah the link to zipped file didn't work as well. I had downloaded the required files

Jul 28

Tim Chan, Barbara Hill3

Jul 28

Thanks. All good! On Wednesday, July 28, 2021 at 7:35:05 AM UTC+10 Barbara Hill wrote: Hello, Yes!

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Thanks. All good! On Wednesday, July 28, 2021 at 7:35:05 AM UTC+10 Barbara Hill wrote: Hello, Yes!

Jul 28

GenePattern Help Forum

Jul 28

Announcement: feature q-value computation in ComparativeMarkerSelection has been restored.

ComparativeMarkerSelection has been fixed to restore the computation of feature q values. https://bit

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Announcement: feature q-value computation in ComparativeMarkerSelection has been restored.

ComparativeMarkerSelection has been fixed to restore the computation of feature q values. https://bit

Jul 28

Viktor, Barbara Hill6

Jul 27

Job 359393 (minor-ish) error

Hi Barbara, Perfect, thank you very much. Best, Viktor On Tuesday, July 27, 2021 at 5:08:37 PM UTC-4

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Job 359393 (minor-ish) error

Hi Barbara, Perfect, thank you very much. Best, Viktor On Tuesday, July 27, 2021 at 5:08:37 PM UTC-4

Jul 27

GenePattern Help Forum

Jul 27

Announcement: AffySTExpressionfileCreator v2 now available

The issues with the previous AffySTExpressionFileCreator Docker image have been resolved. It has also

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Announcement: AffySTExpressionfileCreator v2 now available

The issues with the previous AffySTExpressionFileCreator Docker image have been resolved. It has also

Jul 27

David Lahr, Barbara Hill5

Jul 19

genePattern python API - gsea parameter gene.sets.database no longer a choice

Excellent news!

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genePattern python API - gsea parameter gene.sets.database no longer a choice

Excellent news!

Jul 19

Scott Varney, Ted Liefeld9

Jul 19

Error when running ssGSEA

Hi Ted, I'm not sure why, but when I created a new username without a period between my first and

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Error when running ssGSEA

Hi Ted, I'm not sure why, but when I created a new username without a period between my first and

Jul 19

Gergely, Ted Liefeld3

Jul 19

Out of memory error when running a MutSigCV job online

Thank you for getting back to me! Just trying again has also been my best bet, so I will keep doing

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Out of memory error when running a MutSigCV job online

Thank you for getting back to me! Just trying again has also been my best bet, so I will keep doing

Jul 19

Johanna Szychter, Anthony Castanza3

Jul 14

ssGSEA signature using combine mode

Hi Anthony, Thanks a lot for your answer! I will combine them manually so. Have a great day! Johanna

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ssGSEA signature using combine mode

Hi Anthony, Thanks a lot for your answer! I will combine them manually so. Have a great day! Johanna

Jul 14

Sofya Polyanskaya, Edwin Juarez5

Jul 12

There seems to be some issues rendering the files that GSEAPreranked created, so I recommend you

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There seems to be some issues rendering the files that GSEAPreranked created, so I recommend you

Jul 12

GenePattern Help Forum

Jul 12

Announcement: The server update has completed successfully and regular use of https://cloud.genepattern.org may now resume.

The server update has completed successfully and regular use of https://cloud.genepattern.org may now

unread,

Announcement: The server update has completed successfully and regular use of https://cloud.genepattern.org may now resume.

The server update has completed successfully and regular use of https://cloud.genepattern.org may now

Jul 12

GenePattern Help Forum

Jul 9

Announcement: On Monday, July 12, the main GenePattern server (https://cloud.genepattern.org) will be offline from 10:30 - 11:30 AM PDT (UTC -7) to install an update addressing an issue with file access in some modules.

On Monday, July 12, the main GenePattern server (https://cloud.genepattern.org) will be offline from

unread,

Announcement: On Monday, July 12, the main GenePattern server (https://cloud.genepattern.org) will be offline from 10:30 - 11:30 AM PDT (UTC -7) to install an update addressing an issue with file access in some modules.

On Monday, July 12, the main GenePattern server (https://cloud.genepattern.org) will be offline from

Jul 9

David Lahr, Ted Liefeld6

Jul 9

python API: server error when downloading zip file

Thanks Ted! That worked - much appreciated to have a method to automatically download. On Wednesday,

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python API: server error when downloading zip file

Thanks Ted! That worked - much appreciated to have a method to automatically download. On Wednesday,

Jul 9

Phoebe Chair, Anthony Castanza2

Jul 8

Enquiries regarding S.pombe database used for GSEA analysis

Hi Phoebe, Unfortunately I don't think we're going to be able to help with this one. MSigDB

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Enquiries regarding S.pombe database used for GSEA analysis

Hi Phoebe, Unfortunately I don't think we're going to be able to help with this one. MSigDB

Jul 8

Hareem Ali, Edwin Juarez2

Jul 7

Error when running GISTIC 2.0

Hello, I would suggest posting in the GISTIC forum about this particular question, as that is

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Error when running GISTIC 2.0

Hello, I would suggest posting in the GISTIC forum about this particular question, as that is

Jul 7

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