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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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Swetha Ramadesikan, Ted Liefeld3

2/1/23

GISTIC2.0 error

Ted, thank you so much for your quick response!! That fixed it, I am able to successfully complete

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GISTIC2.0 error

Ted, thank you so much for your quick response!! That fixed it, I am able to successfully complete

2/1/23

Yura SONG, Ted Liefeld2

2/11/20

Hi I think you might have better luck getting help at the GISTIC forum . https://groups.google.com/a/

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troubleshooting

Hi I think you might have better luck getting help at the GISTIC forum . https://groups.google.com/a/

2/11/20

Domenico Somma, Anthony Castanza2

12/10/19

RNAseq rnk file return "A 'chip.platform.file' must be provided for collapse/remap" Error

Hi, To align with changes that we implemented in GSEA Desktop Preranked, version 7 of the module

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RNAseq rnk file return "A 'chip.platform.file' must be provided for collapse/remap" Error

Hi, To align with changes that we implemented in GSEA Desktop Preranked, version 7 of the module

12/10/19

9/30/19

Install R version of GenePattern

Hi, I'm a new learner of this platform. And I am trying to use the platform in the R environment

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Install R version of GenePattern

Hi, I'm a new learner of this platform. And I am trying to use the platform in the R environment

9/30/19

Loreina, Barbara Hill2

9/6/19

Index exceeds matrix dimensions GISTIC

Hello Loreina, The error shows that it can't read your headers, which is because the seg file is

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Index exceeds matrix dimensions GISTIC

Hello Loreina, The error shows that it can't read your headers, which is because the seg file is

9/6/19

Nikho Hizon, Barbara Hill2

7/12/19

Metagene Projection Model could not find or load main class RunR

Hello Nikho, Thank you for bringing this to our attention. The module was not correctly configured to

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Metagene Projection Model could not find or load main class RunR

Hello Nikho, Thank you for bringing this to our attention. The module was not correctly configured to

7/12/19

tang5...@gmail.com

2/17/19

Job attempt duration exceeded timeout

hi, my job ID is 86910 for NMFconsencus, and I have noticed Barbara's replies of this question. i

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Job attempt duration exceeded timeout

hi, my job ID is 86910 for NMFconsencus, and I have noticed Barbara's replies of this question. i

2/17/19

GenePattern Help Forum, Johanna Daily2

2/5/19

What does this GSEA error mean? "GeneSets should have unique names"

thanks, it does seem that when I use a different dataset results are provided thank you! johanna On

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What does this GSEA error mean? "GeneSets should have unique names"

thanks, it does seem that when I use a different dataset results are provided thank you! johanna On

2/5/19

Yongchao Dou, Barbara Hill2

2/4/19

GenePattern cloud error

Hello, My sincere apologies for taking so long to respond. A new version of MutSigCV has been

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GenePattern cloud error

Hello, My sincere apologies for taking so long to respond. A new version of MutSigCV has been

2/4/19

Shixiang Wang, Barbara Hill2

2/4/19

gp_MutSigCV: Permission denied

Hello Shixiang, My sincere apologies for having not responded sooner. An updated version of MutSigCV

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gp_MutSigCV: Permission denied

Hello Shixiang, My sincere apologies for having not responded sooner. An updated version of MutSigCV

2/4/19

Matthew Cserhati, Barbara Hill2

11/20/18

GSEA not working

Hello Matthew, Both of the jobs you cited seem to have been deleted. Were you able to resolve your

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GSEA not working

Hello Matthew, Both of the jobs you cited seem to have been deleted. Were you able to resolve your

11/20/18

Chris C, … Peter Carr6

11/9/18

I can't upload any gct files in any modules

We added more disk capacity. It's ready for new jobs. Thanks again for letting us know. Regards,

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I can't upload any gct files in any modules

We added more disk capacity. It's ready for new jobs. Thanks again for letting us know. Regards,

11/9/18

Théo Hirsch, Barbara Hill2

11/8/18

Error while using MutSigCV on the new cloud server

Hello, Thank you for bringing this to our attention. This module needs to be updated to run in Docker

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Error while using MutSigCV on the new cloud server

Hello, Thank you for bringing this to our attention. This module needs to be updated to run in Docker

11/8/18

Xavier de luca, Barbara Hill2

11/8/18

Error attempting to run MutSigCV on GenePattern

Hello, Can you provide your job id? This will help to determine all the details of how your job was

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Error attempting to run MutSigCV on GenePattern

Hello, Can you provide your job id? This will help to determine all the details of how your job was

11/8/18

6279...@qq.com, Barbara Hill2

10/19/18

No mutation left in MutSigCV

Hello Apologies for the delay in responding. Some members of the team have been out of the office.

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No mutation left in MutSigCV

Hello Apologies for the delay in responding. Some members of the team have been out of the office.

10/19/18

Steve L, … tingting gao7

7/8/20

Not enough mutations to analyze?

Hello Steve, How are you? Have you solved this problem? I have the same probelm with you. Can you

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Not enough mutations to analyze?

Hello Steve, How are you? Have you solved this problem? I have the same probelm with you. Can you

7/8/20

anfal alizai, Barbara Hill5

7/16/18

DAPPLE input problem

Hello Anfal, I was away on vacation and have just returned. Do you have a new job id? Best -Barbara

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DAPPLE input problem

Hello Anfal, I was away on vacation and have just returned. Do you have a new job id? Best -Barbara

7/16/18

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