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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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Harper Tayar, li.dav...@gmail.com3

12/1/25

Re: [genepattern-help:3286] Gabriel is in the neighborhood!!

Hi Harper, Yes we are interested! As a GenePattern user, the most common problem for us is the dirty

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Re: [genepattern-help:3286] Gabriel is in the neighborhood!!

Hi Harper, Yes we are interested! As a GenePattern user, the most common problem for us is the dirty

12/1/25

Dong Gun Oh, … John Liefeld9

11/29/25

A Request for Quota Increase

Hi, I was just going to take another look and it seems the input files for you job are no longer on

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A Request for Quota Increase

Hi, I was just going to take another look and it seems the input files for you job are no longer on

11/29/25

Mohammad Shboul, … John Liefeld4

11/26/25

BAM file around 40 GB

Done. You now have a 50GB quota. Please let us know if/when you no longer need it Ted On Tuesday,

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BAM file around 40 GB

Done. You now have a 50GB quota. Please let us know if/when you no longer need it Ted On Tuesday,

11/26/25

Morgan Roberts, Anthony Castanza4

10/3/25

Error Getting Documentation for ssGSEA

That worked, thanks! On Fri, Oct 3, 2025 at 2:13 PM Anthony Castanza <acas...@cloud.ucsd.edu>

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Error Getting Documentation for ssGSEA

That worked, thanks! On Fri, Oct 3, 2025 at 2:13 PM Anthony Castanza <acas...@cloud.ucsd.edu>

10/3/25

9/27/25

GROUP RATES FOR VENTS CLEANING SERVICES ,Just text/call/WhatsApp me at 321-780-3267

Dear Neighbors, I'm considering organizing a group HVAC cleaning service for our community .I

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GROUP RATES FOR VENTS CLEANING SERVICES ,Just text/call/WhatsApp me at 321-780-3267

Dear Neighbors, I'm considering organizing a group HVAC cleaning service for our community .I

9/27/25

Ted (aka John) Liefeld

8/18/25

Re: [gp-team] Request for Deletion of Uploaded Data

Polina, I have ensured that those job results and their input files have been deleted from our system

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Re: [gp-team] Request for Deletion of Uploaded Data

Polina, I have ensured that those job results and their input files have been deleted from our system

8/18/25

Jayakumar Nair, John Liefeld5

8/13/25

Visualizer issues

Hi Sorry that its still not working. My best guess is that it might still have a certificate issue

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Visualizer issues

Hi Sorry that its still not working. My best guess is that it might still have a certificate issue

8/13/25

junhao zhu, … Thorin Tabor5

8/6/25

Error launching project

One of our notebook servers was stuck. I apologize. The issue has now been fixed. If you retry the

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Error launching project

One of our notebook servers was stuck. I apologize. The issue has now been fixed. If you retry the

8/6/25

Nanette Bishopric, … John Liefeld8

7/17/25

Long wait to start job

Thank you! That makes sense. Apologies for not responding sooner- just got off a long plane flight.

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Long wait to start job

Thank you! That makes sense. Apologies for not responding sooner- just got off a long plane flight.

7/17/25

Andrew Cherniack, … John Liefeld7

7/14/25

GISTIC failed to produce out puts

Thanks On Mon, Jul 14, 2025 at 10:40 AM John Liefeld <jlie...@cloud.ucsd.edu> wrote: Sent you

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GISTIC failed to produce out puts

Thanks On Mon, Jul 14, 2025 at 10:40 AM John Liefeld <jlie...@cloud.ucsd.edu> wrote: Sent you

7/14/25

7/14/25

Re: [gp-team] Download Page not available

Hi, a few months ago we transferred genepattern.org to a new server and new software stack and

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Re: [gp-team] Download Page not available

Hi, a few months ago we transferred genepattern.org to a new server and new software stack and

7/14/25

soumithwork p, John Liefeld2

6/16/25

error after installing module

Hi that looks like an error at run time not an error at the time of module installation. To debug

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error after installing module

Hi that looks like an error at run time not an error at the time of module installation. To debug

6/16/25

Ted (aka John) Liefeld

5/8/25

Re: [gp-team] Log-in error

Courtney, Can you try again and confirm that this is happening repeatedly for you? I have just done a

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Re: [gp-team] Log-in error

Courtney, Can you try again and confirm that this is happening repeatedly for you? I have just done a

5/8/25

Vered Bar, John Liefeld3

4/29/25

Thanks!! Sent from my iPhone On 29 Apr 2025, at 17:48, John Liefeld <jlie...@cloud.ucsd.edu>

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Thanks!! Sent from my iPhone On 29 Apr 2025, at 17:48, John Liefeld <jlie...@cloud.ucsd.edu>

4/29/25

Regan Odongo, … Kyle Starost13

4/28/25

Using GenePattern

Hi Ted, Thank you so much for the help! I changed it to a higher memory (12GB) and it worked. Much

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Using GenePattern

Hi Ted, Thank you so much for the help! I changed it to a higher memory (12GB) and it worked. Much

4/28/25

Subhojit paul, Ted Liefeld2

4/2/25

DESeq2 ver 3 issues

Hi Sorry that this was missed when you sent this to gp-help originally. Unfortunately the job has

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DESeq2 ver 3 issues

Hi Sorry that this was missed when you sent this to gp-help originally. Unfortunately the job has

4/2/25

Alexandra Glathar, Ted Liefeld3

3/25/25

Error running SurvivalDifference and CoxRegression

Hi, SurvivalDifference is running again using the test data from the documentation (https://datasets.

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Error running SurvivalDifference and CoxRegression

Hi, SurvivalDifference is running again using the test data from the documentation (https://datasets.

3/25/25

JESSIE HOLLINGSWORTH, Ted Liefeld2

3/13/25

Increased storage

Hi, I have increased it back, sorry for the inconvenience. We upgraded the server last week, and

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Increased storage

Hi, I have increased it back, sorry for the inconvenience. We upgraded the server last week, and

3/13/25

Jessie Hollingsworth, Ted Liefeld4

3/5/25

Increased storage

Please refresh the page, you should see the update now. I assumed you were on cloud.genepattern.org

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Increased storage

Please refresh the page, you should see the update now. I assumed you were on cloud.genepattern.org

3/5/25

Ted (aka John) Liefeld

2/26/25

Re: [gp-team] Log in error

Courtney, Sorry this is happening to you. Starting with the second error, the emails are case

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Re: [gp-team] Log in error

Courtney, Sorry this is happening to you. Starting with the second error, the emails are case

2/26/25

2/19/25

pmeTPM RNAseq data for running GSEA, ssGSEA and ssGSEA-ROC

Hi, My name is Lilian Inoue. I have a RNAseq dataset where the resulting reads were aligned to the

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pmeTPM RNAseq data for running GSEA, ssGSEA and ssGSEA-ROC

Hi, My name is Lilian Inoue. I have a RNAseq dataset where the resulting reads were aligned to the

2/19/25

Pierre Laplante, Ted Liefeld3

2/17/25

Hi again, I don't yet have a fix but the problem seems to be that one or more of the files

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Hi again, I don't yet have a fix but the problem seems to be that one or more of the files

2/17/25

2/13/25

Help with ssGSEA errors with input .gct files

Hello, my input .gct gene expression files produce constant error files and process terminations on

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Help with ssGSEA errors with input .gct files

Hello, my input .gct gene expression files produce constant error files and process terminations on

2/13/25

liat anabel, Andrew Cherniack9

1/31/25

Cross chromosomes error in GISTIC2.0 v. 6.15.30 unsing GenePattern public server

Thank you I will check this. Best regards, Liat בתאריך יום ו׳, 31 בינו׳ 2025, 23:39, מאת 'Andrew

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Cross chromosomes error in GISTIC2.0 v. 6.15.30 unsing GenePattern public server

Thank you I will check this. Best regards, Liat בתאריך יום ו׳, 31 בינו׳ 2025, 23:39, מאת 'Andrew

1/31/25

Shota Kato, Andrew Cherniack3

1/28/25

GISTIC2 with public server

Hello Andy, I used the default parameters with the broad analysis option. I attached the input seg

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GISTIC2 with public server

Hello Andy, I used the default parameters with the broad analysis option. I attached the input seg

1/28/25

Anne Van Arsdale, Jens Luebeck2

1/21/25

Amplicon Architect

Hi Anne, Thanks for reaching out with this bug report. The issue is related to the use of the

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Amplicon Architect

Hi Anne, Thanks for reaching out with this bug report. The issue is related to the use of the

1/21/25

ravi, Michael Reich5

1/14/25

AmpliconSeq - FASTQ files - Analysis Tools

Thank you, Michael. Looks like the input MAFs are only from WGS or WES but not from Targeted Amplicon

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AmpliconSeq - FASTQ files - Analysis Tools

Thank you, Michael. Looks like the input MAFs are only from WGS or WES but not from Targeted Amplicon

1/14/25

Xiao LIANG, … John Liefeld7

12/10/24

AuDIT is not in the module list

Hi John and Ted, Thanks for the kind help! Best Regards, Xiao On Wed, Dec 11, 2024 at 6:02 AM John

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AuDIT is not in the module list

Hi John and Ted, Thanks for the kind help! Best Regards, Xiao On Wed, Dec 11, 2024 at 6:02 AM John

12/10/24

Sumithra Sankararaman, Ted Liefeld2

12/2/24

error running mutsigcv

I suggest you contact the authors of the method at mutsi...@broadinstitute.org and ask them. Hope

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error running mutsigcv

I suggest you contact the authors of the method at mutsi...@broadinstitute.org and ask them. Hope

12/2/24

11/15/24

Is it still possible to run ABSOLUTE?

Hi, we'd like to run ABSOLUTE for tumour purity estimation but I can't seem to find/access

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Is it still possible to run ABSOLUTE?

Hi, we'd like to run ABSOLUTE for tumour purity estimation but I can't seem to find/access

11/15/24

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