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.

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Happy posting!

-The GenePattern team

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sunand...@gmail.com, Ted Liefeld2

Mar 15

How to extract the Cancer Cell Fraction for copy number lesions (eg. 8q23.3) from ABSOLUTE output?

Hi unfortunately we do not have any experience with Absolute in the GenePattern team. I asked a

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How to extract the Cancer Cell Fraction for copy number lesions (eg. 8q23.3) from ABSOLUTE output?

Hi unfortunately we do not have any experience with Absolute in the GenePattern team. I asked a

Mar 15

Conrad, Ted Liefeld4

Mar 14

Issues with DESeq2 module cls file

Thank you very much! On Tuesday, March 14, 2023 at 1:23:22 AM UTC+8 Ted Liefeld wrote: Hi again, one

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Issues with DESeq2 module cls file

Thank you very much! On Tuesday, March 14, 2023 at 1:23:22 AM UTC+8 Ted Liefeld wrote: Hi again, one

Mar 14

Hai Tran, … David Eby4

Mar 1

Error with ssGSEA (job ID: 496000)

Thanks Ted and David. Indeed there is one line having ",". Sometime "copy paste"

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Error with ssGSEA (job ID: 496000)

Thanks Ted and David. Indeed there is one line having ",". Sometime "copy paste"

Mar 1

Andrew Cherniack, tmt...@cloud.ucsd.edu9

Feb 22

GISTIC Refgene files

Thanks again! Andy On Wed, Feb 22, 2023 at 3:47 PM tmt...@cloud.ucsd.edu <tmt...@cloud.ucsd.edu

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GISTIC Refgene files

Thanks again! Andy On Wed, Feb 22, 2023 at 3:47 PM tmt...@cloud.ucsd.edu <tmt...@cloud.ucsd.edu

Feb 22

John L Pulice, … Hanie Azari9

Feb 14

thanks for your reply thorin 🌹 On Tue, Feb 14, 2023, 10:23 PM tmt...@cloud.ucsd.edu <tmtabor@cloud

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thanks for your reply thorin 🌹 On Tue, Feb 14, 2023, 10:23 PM tmt...@cloud.ucsd.edu <tmtabor@cloud

Feb 14

Katia Nones, … tmt...@cloud.ucsd.edu3

Feb 13

We have just updated the GISTIC_2.0 module. Please try again. Thorin Tabor GenePattern Team On Monday

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We have just updated the GISTIC_2.0 module. Please try again. Thorin Tabor GenePattern Team On Monday

Feb 13

Mingyuan Wan, … Ted Liefeld6

Feb 13

tximport.DESeq2 issue

Please give it another try now. We have a new version (3.8) where the parameter is no longer required

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tximport.DESeq2 issue

Please give it another try now. We have a new version (3.8) where the parameter is no longer required

Feb 13

Matt Moravec, … Hanie Azari4

Feb 13

Gistic2.0 Segment overlap error

Dear Matt, I also face this issue, did you find any solution? thanks, Hanieh A On Monday, June 29,

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Gistic2.0 Segment overlap error

Dear Matt, I also face this issue, did you find any solution? thanks, Hanieh A On Monday, June 29,

Feb 13

Amy, … Hela SASSI12

Feb 5

NMFConsensus error: 'memory not mapped'

Hi Ted, Thank you for your reply. but I did not get any response on the gistic forum Best regards

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NMFConsensus error: 'memory not mapped'

Hi Ted, Thank you for your reply. but I did not get any response on the gistic forum Best regards

Feb 5

Swetha Ramadesikan, Ted Liefeld3

Feb 1

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

Feb 1

Hai Tran, edh...@cloud.ucsd.edu3

Jan 23

NTP running error!

Hi Edwin, Thank you very much! it works now;)! Hai edh...@cloud.ucsd.edu schrieb am Freitag, 20.

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NTP running error!

Hi Edwin, Thank you very much! it works now;)! Hai edh...@cloud.ucsd.edu schrieb am Freitag, 20.

Jan 23

DIANA, Ted Liefeld4

Jan 3

Gene Pattern dapple pending? bug job results/queue?

Thank you for getting the queue working again! On Tuesday, January 3, 2023 at 1:11:06 PM UTC-8 lie...

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Gene Pattern dapple pending? bug job results/queue?

Thank you for getting the queue working again! On Tuesday, January 3, 2023 at 1:11:06 PM UTC-8 lie...

Jan 3

JH, Michael Reich2

Jan 3

NTP interpretation help

Hi Julia, Apologies for the delay in responding. You are correct - the "correlation" option

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NTP interpretation help

Hi Julia, Apologies for the delay in responding. You are correct - the "correlation" option

Jan 3

seika...@gmail.com, edh...@cloud.ucsd.edu2

Jan 3

Seurat.QC error

Hi, Can you try running the job again to see if you get the same error? It might be an intermittent

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Seurat.QC error

Hi, Can you try running the job again to see if you get the same error? It might be an intermittent

Jan 3

Sam Preston, … Anthony Castanza9

12/1/22

Error updating upload file record for file 'tmp': null

Hi Sam, Yes this is expected, GSEA and its variants like ssGSEA are designed to use the information

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Error updating upload file record for file 'tmp': null

Hi Sam, Yes this is expected, GSEA and its variants like ssGSEA are designed to use the information

12/1/22

Erbol Nishanov, Ted Liefeld2

11/30/22

File formatting

Hi the file transfer error might not be the format. There is a bug that is fixed in the next release

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File formatting

Hi the file transfer error might not be the format. There is a bug that is fixed in the next release

11/30/22

Ishaar Ganesan, … Ted Liefeld4

11/28/22

What does this error regarding marker less than smooth length and chromosome smoothing mean? What can I do to fix/bypass this error?

You should ask this question on the GISTIC forum, https://groups.google.com/a/broadinstitute.org/

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What does this error regarding marker less than smooth length and chromosome smoothing mean? What can I do to fix/bypass this error?

You should ask this question on the GISTIC forum, https://groups.google.com/a/broadinstitute.org/

11/28/22

Sruthi S, tmt...@cloud.ucsd.edu2

11/21/22

Hello Sruthi, We will add this as a feature request, but unfortunately Mutiplot Studio does not

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Hello Sruthi, We will add this as a feature request, but unfortunately Mutiplot Studio does not

11/21/22

Neelam Shinde, … Anthony Castanza8

11/19/22

*** caught segfault *** address 0x7f7ca03d7618, cause 'invalid permissions' error

Thank you for your reply Anthony. It is very helpful. I will wait on the update regarding the issue

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*** caught segfault *** address 0x7f7ca03d7618, cause 'invalid permissions' error

Thank you for your reply Anthony. It is very helpful. I will wait on the update regarding the issue

11/19/22

Patrick Jonker, Ted Liefeld4

11/10/22

tmp: null error (403) when trying to run GSEAPRERANKED

Patrick, give it another try now and let me know how it goes Ted On Wednesday, November 9, 2022 at 10

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tmp: null error (403) when trying to run GSEAPRERANKED

Patrick, give it another try now and let me know how it goes Ted On Wednesday, November 9, 2022 at 10

11/10/22

Sumithra Sankararaman, Ted Liefeld3

11/9/22

Thank you, Ted. I will contact the google group you have referenced. Sumithra On Mon, Nov 7, 2022 at

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Thank you, Ted. I will contact the google group you have referenced. Sumithra On Mon, Nov 7, 2022 at

11/9/22

Amelia Jones, Ted Liefeld6

11/6/22

GISTIC2.0 Out put error

Ted, Thanks so much, I checked the error message you mentioned and I'm guessing it's because

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GISTIC2.0 Out put error

Ted, Thanks so much, I checked the error message you mentioned and I'm guessing it's because

11/6/22

Natalia V, Ted Liefeld3

10/27/22

TCGAImporter Error Message

Natalia I think there are a few problems here and it may be necessary for you to download outside of

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TCGAImporter Error Message

Natalia I think there are a few problems here and it may be necessary for you to download outside of

10/27/22

Andi L., Ted Liefeld7

10/27/22

GISTIC2.0 internal server errors

Andi the errors sound like memory was the problem. My guess is that you don't need to specify the

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GISTIC2.0 internal server errors

Andi the errors sound like memory was the problem. My guess is that you don't need to specify the

10/27/22

Vithurran Thavarajah, … Anthony Castanza7

10/26/22

ssGSEA help (ID: 471802. ssGSEA)

Thanks Anthony and Ted, Apologies for the late reply. Yes it seems to be a fault on my end with the .

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ssGSEA help (ID: 471802. ssGSEA)

Thanks Anthony and Ted, Apologies for the late reply. Yes it seems to be a fault on my end with the .

10/26/22

Sara Soria, Thorin Tabor5

10/25/22

Hello, You can find the source for the FLAME modules at the following links: FlamePreprocess: https:/

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Hello, You can find the source for the FLAME modules at the following links: FlamePreprocess: https:/

10/25/22

Mario Ezquerra, Anthony Castanza3

10/25/22

ssGSEA ROC module error message

Hi Mario, Quick follow up. I have a workaround for you. If you change the names of your gene sets to

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ssGSEA ROC module error message

Hi Mario, Quick follow up. I have a workaround for you. If you change the names of your gene sets to

10/25/22

Mario Ezquerra, Ted Liefeld3

10/21/22

help SVM prediction

Thanks! it works El mié, 5 oct 2022 a las 18:37, Ted Liefeld (<lie...@broadinstitute.org>)

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help SVM prediction

Thanks! it works El mié, 5 oct 2022 a las 18:37, Ted Liefeld (<lie...@broadinstitute.org>)

10/21/22

Samyukta Mallick, Anthony Castanza3

10/20/22

GSEAPreranked floating point number parsing error message

Thank you! I completely forgot that step. It worked now. On Oct 20, 2022, at 1:08 PM, Anthony

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GSEAPreranked floating point number parsing error message

Thank you! I completely forgot that step. It worked now. On Oct 20, 2022, at 1:08 PM, Anthony

10/20/22

Jaishree Tripathi, … Anthony Castanza8

10/18/22

Hi Jaishree, To follow up Ted's answer, the results in the .PROJ.gct file are the enrichment

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Hi Jaishree, To follow up Ted's answer, the results in the .PROJ.gct file are the enrichment

10/18/22

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