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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Sam Preston, … Anthony Castanza9

Dec 1

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

Dec 1

Erbol Nishanov, Ted Liefeld2

Nov 30

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

Nov 30

Ishaar Ganesan, … Ted Liefeld4

Nov 28

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/

Nov 28

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

Nov 21

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

Nov 21

Neelam Shinde, … Anthony Castanza8

Nov 19

*** 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

Nov 19

Patrick Jonker, Ted Liefeld4

Nov 10

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

Nov 10

Sumithra Sankararaman, Ted Liefeld3

Nov 9

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

Nov 9

Amelia Jones, Ted Liefeld6

Nov 6

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

Nov 6

Natalia V, Ted Liefeld3

Oct 27

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

Oct 27

Andi L., Ted Liefeld7

Oct 27

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

Oct 27

Vithurran Thavarajah, … Anthony Castanza7

Oct 26

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 .

Oct 26

Sara Soria, Thorin Tabor5

Oct 25

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:/

Oct 25

Mario Ezquerra, Anthony Castanza3

Oct 25

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

Oct 25

Mario Ezquerra, Ted Liefeld3

Oct 21

help SVM prediction

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

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help SVM prediction

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

Oct 21

Samyukta Mallick, Anthony Castanza3

Oct 20

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

Oct 20

Jaishree Tripathi, … Anthony Castanza8

Oct 18

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

Oct 18

二哈李, 王建东3

Oct 13

Questions About the NTP Module input features file

ok, thanks for your answer. On Sunday, October 9, 2022 at 10:57:58 PM UTC+8 19797...@qq.com wrote: At

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Questions About the NTP Module input features file

ok, thanks for your answer. On Sunday, October 9, 2022 at 10:57:58 PM UTC+8 19797...@qq.com wrote: At

Oct 13

GenePattern User, … Ted Liefeld6

Oct 10

MutSigCV, GenePattern, File Transfer Error

I have sent you a private email to set up a zoom call when you have time today. I see that you have

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MutSigCV, GenePattern, File Transfer Error

I have sent you a private email to set up a zoom call when you have time today. I see that you have

Oct 10

Jayakumar Nair, Ted Liefeld3

Oct 3

leading edge visualizer not working

THank you. I did use the GSEA application and it worked fine. Thank you Jay /////////////////////////

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leading edge visualizer not working

THank you. I did use the GSEA application and it worked fine. Thank you Jay /////////////////////////

Oct 3

王东, Ted Liefeld4

Sep 29

question about NearestTemplatePrediction

Thank you, I tried this and it successfully worked. wjd 在2022年9月29日星期四 UTC+8 00:45:02<lie...@

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question about NearestTemplatePrediction

Thank you, I tried this and it successfully worked. wjd 在2022年9月29日星期四 UTC+8 00:45:02<lie...@

Sep 29

Sep 28

the sample files fo NTP

Hi, Who has NTP sample files? Can you send me a copy. Thank you wjd

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the sample files fo NTP

Hi, Who has NTP sample files? Can you send me a copy. Thank you wjd

Sep 28

eleni, … myxu.china7

Sep 27

GSEAPreranked error message

Many thanks, yes it works now both with v7.3.5 and 7.3.7. Thanks again for looking into it, Eleni On

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GSEAPreranked error message

Many thanks, yes it works now both with v7.3.5 and 7.3.7. Thanks again for looking into it, Eleni On

Sep 27

Sep 26

GISTIC2.0 error message

Dear GenePattern team I met some errors when I run GISTIC2.0. GenePattern Server error preparing job

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GISTIC2.0 error message

Dear GenePattern team I met some errors when I run GISTIC2.0. GenePattern Server error preparing job

Sep 26

Hela SASSI, edh...@cloud.ucsd.edu3

Sep 23

GISTIC2 error message

Hi Hela, We think the error was due to an intermittent issue. I recommend re-running your job and let

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GISTIC2 error message

Hi Hela, We think the error was due to an intermittent issue. I recommend re-running your job and let

Sep 23

Camilla Ceccarani, mmr...@cloud.ucsd.edu3

Sep 19

MutSig2CV error: silent and nonsilent rates are too different

Thank you Michael, although I couldn't find any solution to my problem and that forum has not

unread,

MutSig2CV error: silent and nonsilent rates are too different

Thank you Michael, although I couldn't find any solution to my problem and that forum has not

Sep 19

Nik, Ted Liefeld2

Sep 14

SNP Copy Number and Loss of Heterozygosity Estimation public pipeline

Hi With respect to your question 1, it looks like the links to the datasets at the Broad Institute

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SNP Copy Number and Loss of Heterozygosity Estimation public pipeline

Hi With respect to your question 1, it looks like the links to the datasets at the Broad Institute

Sep 14

Sep 12

Re: [gp-team] GenePattern access

Hi There was a problem with some automatic maintenance updates that were applied last night. The

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Re: [gp-team] GenePattern access

Hi There was a problem with some automatic maintenance updates that were applied last night. The

Sep 12

Angelussong, Ted Liefeld3

Sep 9

Hi Ted, Thanks for your reply! One of the failed job IDs was 460602. Last night I think I solved this

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Hi Ted, Thanks for your reply! One of the failed job IDs was 460602. Last night I think I solved this

Sep 9

Jihong Tang, Ted Liefeld3

Sep 6

Questions About the GISTIC2 Module output amp plot file

Hi Thank you for the instructions. Best Jihong On Wed, Sep 7, 2022 at 1:38 AM Ted Liefeld <liefeld

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Questions About the GISTIC2 Module output amp plot file

Hi Thank you for the instructions. Best Jihong On Wed, Sep 7, 2022 at 1:38 AM Ted Liefeld <liefeld

Sep 6

Sumithra Sankararaman, Ted Liefeld4

Sep 2

error in ssgsea module

Sumithra at the bottom of the normal parameters sections, you should see a collapsed section called

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error in ssgsea module

Sumithra at the bottom of the normal parameters sections, you should see a collapsed section called

Sep 2

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