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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3:39 PM

Error when trying to run GSEA pre-ranked

ps. I found this stackoverflow that might be relevant: https://stackoverflow.com/questions/55702196/

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Error when trying to run GSEA pre-ranked

ps. I found this stackoverflow that might be relevant: https://stackoverflow.com/questions/55702196/

3:39 PM

Jan 21

tximport.DESeq2 error

Last update: I reran the job that successfully completed before (job 402939) with the same input

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tximport.DESeq2 error

Last update: I reran the job that successfully completed before (job 402939) with the same input

Jan 21

Sruthi S, … Barbara Hill26

Jan 18

Displaying Error

Hi Sruthi, I would suggest trying CollapseDataset. You can use this on the GCT output from DESeq2.

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Displaying Error

Hi Sruthi, I would suggest trying CollapseDataset. You can use this on the GCT output from DESeq2.

Jan 18

Sruthi S, Barbara Hill7

Jan 14

Displaying error

Hi Sruthi, Please see the file formats guide for more information: https://genepattern.org/file-

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Displaying error

Hi Sruthi, Please see the file formats guide for more information: https://genepattern.org/file-

Jan 14

白澤昌之, Anthony Castanza3

Jan 6

about using TPM with ssGSEA

Dear Anthony, Thanks a lot for your answer! I'm going to try both patterns. Masayuki Shirasawa

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about using TPM with ssGSEA

Dear Anthony, Thanks a lot for your answer! I'm going to try both patterns. Masayuki Shirasawa

Jan 6

mko, Anthony Castanza2

Jan 4

ssGSEA input (gene expression data is not available)

Hi MJ, Without knowing the details of your ranking metric its difficult to say if it would be

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ssGSEA input (gene expression data is not available)

Hi MJ, Without knowing the details of your ranking metric its difficult to say if it would be

Jan 4

Viktor, Anthony Castanza5

12/29/21

Salmon and DESeq2

Hi Anthony, Sounds good, thank you for your help. Viktor On Wednesday, December 29, 2021 at 5:01:01

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Salmon and DESeq2

Hi Anthony, Sounds good, thank you for your help. Viktor On Wednesday, December 29, 2021 at 5:01:01

12/29/21

12/27/21

How to creat coverage file the input file required by MutSigCV

Excuse me: I am trying to used MutSigCV to analyze my own WES data. Several input files were required

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How to creat coverage file the input file required by MutSigCV

Excuse me: I am trying to used MutSigCV to analyze my own WES data. Several input files were required

12/27/21

GenePattern Help Forum

12/21/21

Announcement: GenePattern Coverage and Support December 23, 2021 - January 2, 2022

From December 23, 2021, through January 2, 2022, the GenePattern team will be out of the office for

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Announcement: GenePattern Coverage and Support December 23, 2021 - January 2, 2022

From December 23, 2021, through January 2, 2022, the GenePattern team will be out of the office for

12/21/21

Laurie Baert, … Edwin Juarez14

12/17/21

Hi Laurie, Take a look at this GenePattern Notebook which has a simple implementation of a volcano

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Hi Laurie, Take a look at this GenePattern Notebook which has a simple implementation of a volcano

12/17/21

Sara Haddock, Thorin Tabor3

12/16/21

GenePattern R package?

ok, that makes sense. Can the Programmers' Guide be edited to reflect that? I'm not the only

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GenePattern R package?

ok, that makes sense. Can the Programmers' Guide be edited to reflect that? I'm not the only

12/16/21

Sara Haddock, Anthony Castanza3

12/16/21

Issue with custom color palette in HierarchicalClusteringImage module

Ahh, so simple! Thank you Anthony!! On Thursday, December 16, 2021 at 2:42:26 PM UTC-5 Anthony

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Issue with custom color palette in HierarchicalClusteringImage module

Ahh, so simple! Thank you Anthony!! On Thursday, December 16, 2021 at 2:42:26 PM UTC-5 Anthony

12/16/21

12/16/21

Re: [gp-team] Sign in issue

Hi Usually this is because the password email is being filtered out by a spam filter. Please try

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Re: [gp-team] Sign in issue

Hi Usually this is because the password email is being filtered out by a spam filter. Please try

12/16/21

GenePattern Help Forum

12/13/21

Announcement: GParc website is now deprecated.

As of Dec 13, 2021, we have deprecated the GParc website. GParc modules are still available in the

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Announcement: GParc website is now deprecated.

As of Dec 13, 2021, we have deprecated the GParc website. GParc modules are still available in the

12/13/21

12/9/21

Le jeudi 9 décembre 2021 à 13:57:21 UTC-5, Laurie Baert a écrit : Hi, I ran HTseq count from my

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Le jeudi 9 décembre 2021 à 13:57:21 UTC-5, Laurie Baert a écrit : Hi, I ran HTseq count from my

12/9/21

Laurie Baert, … Anthony Castanza7

12/8/21

Hi Laurie, I ran some tests and It looks like the issue here is in the "Job Options"

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Hi Laurie, I ran some tests and It looks like the issue here is in the "Job Options"

12/8/21

GenePattern Help Forum

12/6/21

Announcement: cloud.genepattern.org upgrade today - including support for GLOBUS file transfers!

TODAY, Dec 6, the main GenePattern server (https://cloud.genepattern.org) will be offline from 2 - 3

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Announcement: cloud.genepattern.org upgrade today - including support for GLOBUS file transfers!

TODAY, Dec 6, the main GenePattern server (https://cloud.genepattern.org) will be offline from 2 - 3

12/6/21

carlamon...@gmail.com, Ted Liefeld2

11/29/21

There was an unexpected file transfer error while submitting your job. Please check your network connection and try to submit again or use the Uploader in the Files tab.

I am sorry that you are having problems with GenePattern. The error you are seeing is typically an

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There was an unexpected file transfer error while submitting your job. Please check your network connection and try to submit again or use the Uploader in the Files tab.

I am sorry that you are having problems with GenePattern. The error you are seeing is typically an

11/29/21

shiyong li, 11699259922

11/17/21

Question aobut GISTIC2 amp or del qplot?

您好，邮件已收到~ 我会尽快向您回复邮件

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Question aobut GISTIC2 amp or del qplot?

您好，邮件已收到~ 我会尽快向您回复邮件

11/17/21

신동윤, … D R Mani5

11/8/21

[AuDIT] Module for proteomic analysis_ we could find the module in the public web server

Hello, I'll try and have it ready by the end of Nov. -- Mani DR Mani, Ph.D. Director of

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[AuDIT] Module for proteomic analysis_ we could find the module in the public web server

Hello, I'll try and have it ready by the end of Nov. -- Mani DR Mani, Ph.D. Director of

11/8/21

Ifra Saifi, … 11699259925

11/7/21

Trouble shooting in registering for gene pattern notebook account

您好，邮件已收到~ 我会尽快向您回复邮件

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Trouble shooting in registering for gene pattern notebook account

您好，邮件已收到~ 我会尽快向您回复邮件

11/7/21

Tyler Sagendorf, … Anthony Castanza3

11/4/21

PTM-SEA: min overlap doesn't filter results

Hello, While GenePattern offers a platform for running PTM-SEA, we don't actually develop it. I

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PTM-SEA: min overlap doesn't filter results

Hello, While GenePattern offers a platform for running PTM-SEA, we don't actually develop it. I

11/4/21

Brendon Price, Ted Liefeld2

11/2/21

Error uploading idat files for CNV analysis

Brendon, I am sorry that you are having problems with GenePattern. The error you are seeing is

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Error uploading idat files for CNV analysis

Brendon, I am sorry that you are having problems with GenePattern. The error you are seeing is

11/2/21

casxue, Barbara Hill2

10/20/21

MutSigCV: mutation_type_dictionary_file is missing error despite providing file

Hello, The issue is that you have changed a substitution variable that GenePattern needs, in order to

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MutSigCV: mutation_type_dictionary_file is missing error despite providing file

Hello, The issue is that you have changed a substitution variable that GenePattern needs, in order to

10/20/21

Daryl Griffin, Anthony Castanza2

10/18/21

Job Number: 385797

Hi Daryl, This dataset is from a microarray platform (GSE72865 is tagged as Platform: GPL10558

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Job Number: 385797

Hi Daryl, This dataset is from a microarray platform (GSE72865 is tagged as Platform: GPL10558

10/18/21

archana bhardwaj, Ted Liefeld2

10/8/21

submap : unexpected file transfer error

Archana we have seen this happen twice before but have not yet been able to determine the cause. Can

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submap : unexpected file transfer error

Archana we have seen this happen twice before but have not yet been able to determine the cause. Can

10/8/21

10/7/21

Missing reCAPTCHA response

Dear genepattern team， Recently, when I registered an account on https://cloud.genepattern.org, the

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Missing reCAPTCHA response

Dear genepattern team， Recently, when I registered an account on https://cloud.genepattern.org, the

10/7/21

IzzyD, Ted Liefeld3

10/7/21

Hi Ted, Thanks for getting back to me. I tried again the next day (the same job) and it worked. The

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Hi Ted, Thanks for getting back to me. I tried again the next day (the same job) and it worked. The

10/7/21

carlamon...@gmail.com, Ted Liefeld2

10/4/21

Carla, I responded to you via the other email you sent in to our old help email address. Have you

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Carla, I responded to you via the other email you sent in to our old help email address. Have you

10/4/21

Roser Pinyol, David Eby3

9/30/21

CollapseDataset Module

Fantastic! Many thanks for this clarification. Best, R El dia dimecres, 29 de setembre de 2021 a les

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CollapseDataset Module

Fantastic! Many thanks for this clarification. Best, R El dia dimecres, 29 de setembre de 2021 a les

9/30/21

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