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GenePattern Help Forum

1–30 of 905

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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soumithwork p, John Liefeld2

Jun 16

error after installing module

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

unread,

error after installing module

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

Jun 16

Ted (aka John) Liefeld

May 8

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

unread,

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

May 8

Vered Bar, John Liefeld3

Apr 29

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

unread,

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

Apr 29

Regan Odongo, … Kyle Starost13

Apr 28

Using GenePattern

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

unread,

Using GenePattern

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

Apr 28

Subhojit paul, Ted Liefeld2

Apr 2

DESeq2 ver 3 issues

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

unread,

DESeq2 ver 3 issues

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

Apr 2

Alexandra Glathar, Ted Liefeld3

Mar 25

Error running SurvivalDifference and CoxRegression

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

unread,

Error running SurvivalDifference and CoxRegression

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

Mar 25

JESSIE HOLLINGSWORTH, Ted Liefeld2

Mar 13

Increased storage

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

unread,

Increased storage

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

Mar 13

Jessie Hollingsworth, Ted Liefeld4

Mar 5

Increased storage

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

unread,

Increased storage

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

Mar 5

Ted (aka John) Liefeld

Feb 26

Re: [gp-team] Log in error

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

unread,

Re: [gp-team] Log in error

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

Feb 26

Feb 19

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

unread,

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

Feb 19

Pierre Laplante, Ted Liefeld3

Feb 17

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

unread,

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

Feb 17

Feb 13

Help with ssGSEA errors with input .gct files

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

unread,

Help with ssGSEA errors with input .gct files

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

Feb 13

liat anabel, Andrew Cherniack9

Jan 31

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

unread,

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

Jan 31

Shota Kato, Andrew Cherniack3

Jan 28

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

Jan 28

Anne Van Arsdale, Jens Luebeck2

Jan 21

Amplicon Architect

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

unread,

Amplicon Architect

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

Jan 21

ravi, Michael Reich5

Jan 14

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

Jan 14

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

unread,

error running mutsigcv

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

12/2/24

Mohammad Shboul, Ted Liefeld2

11/20/24

BAM file around 40 GB

Hi, I can expand your quota, but I will need your username to do so. I did not find an account on

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BAM file around 40 GB

Hi, I can expand your quota, but I will need your username to do so. I did not find an account on

11/20/24

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

Imran Noorani, Michael Reich3

10/23/24

Hi Michael This is very helpful thank you Best wishes Imran Sent from my iPhone On 22 Oct 2024, at 22

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Hi Michael This is very helpful thank you Best wishes Imran Sent from my iPhone On 22 Oct 2024, at 22

10/23/24

Bob Zimmermann, Anthony Castanza3

10/14/24

Normalization Strategies for ssGSEA

Thanks Anthony. This is helpful! Let me know if you hear anything further. On Friday, October 11,

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Normalization Strategies for ssGSEA

Thanks Anthony. This is helpful! Let me know if you hear anything further. On Friday, October 11,

10/14/24

Alex Waldman, Anthony Castanza2

10/11/24

Gene Priorization

Hi Alex, I'm not entirely sure what you're referring to here. We don't, to my knowledge,

unread,

Gene Priorization

Hi Alex, I'm not entirely sure what you're referring to here. We don't, to my knowledge,

10/11/24

Ariyan, Anthony Castanza4

10/9/24

Missing genesets in ssGSEA Output Despite Being Present in Input Files

Hi Airyan, That's my bad, ssGSEA is actually located in the GSEA org repository not the

unread,

Missing genesets in ssGSEA Output Despite Being Present in Input Files

Hi Airyan, That's my bad, ssGSEA is actually located in the GSEA org repository not the

10/9/24

ali pirani, John Liefeld2

10/8/24

Subscripted assignment dimension mismatch.

Hi, I took a quick look but am not familiar enough with MutSigCV to be able to help with this. I

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Subscripted assignment dimension mismatch.

Hi, I took a quick look but am not familiar enough with MutSigCV to be able to help with this. I

10/8/24

Jennifer Diaz, Ted Liefeld10

10/4/24

Jennifer, We don't have any prepared instructions but it should be possible to do assuming you

unread,

Jennifer, We don't have any prepared instructions but it should be possible to do assuming you

10/4/24

ravi, Michael Reich5

9/24/24

Thank you, Michael. Best regards, Ravi. On Wed, 25 Sept 2024 at 06:31, Michael Reich <mmreich@

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Thank you, Michael. Best regards, Ravi. On Wed, 25 Sept 2024 at 06:31, Michael Reich <mmreich@

9/24/24

ravi, Ted Liefeld2

9/23/24

Job id: 604988 - Error

Ravi, based off the error it looks like the csv files are possibly corrupted or are somehow

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Job id: 604988 - Error

Ravi, based off the error it looks like the csv files are possibly corrupted or are somehow

9/23/24

bri colletti, Michael Reich2

9/23/24

ExpressionFileCreator Error

Hi Bri, Can you describe the problems you are having? Also, if you were using the public GenePattern

unread,

ExpressionFileCreator Error

Hi Bri, Can you describe the problems you are having? Also, if you were using the public GenePattern

9/23/24

Admita, edh...@cloud.ucsd.edu2

9/20/24

Hi, What's the Job ID for this result? Edwin On Thursday, September 19, 2024 at 9:41:16 PM UTC-7

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Hi, What's the Job ID for this result? Edwin On Thursday, September 19, 2024 at 9:41:16 PM UTC-7

9/20/24

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