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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Fan Ge, Ted Liefeld2

Oct 2

Error in GISTIC2.0 GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

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Error in GISTIC2.0 GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

Oct 2

槐笑栀, … Andrew Cherniack7

Sep 28

what's the problem about the online GISTIC2 with this output?

thanks Andy, I delete all of the overlaps samples which were consisted by sample "TCGA-CV-6955-

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what's the problem about the online GISTIC2 with this output?

thanks Andy, I delete all of the overlaps samples which were consisted by sample "TCGA-CV-6955-

Sep 28

Peipei Wang, … 槐笑栀11

Sep 28

GISTIC 2.0 input error detected: Data missing in segment file

Hi Peipei! I meet the same problem with you! In my first-time input seg-file, it's a problem that

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GISTIC 2.0 input error detected: Data missing in segment file

Hi Peipei! I meet the same problem with you! In my first-time input seg-file, it's a problem that

Sep 28

yulu shi, Ted Liefeld3

Sep 27

Trouble with NTP(nearest template prediction)

Thanks After I change the input.features file into tab separated version, and delete the leftmost

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Trouble with NTP(nearest template prediction)

Thanks After I change the input.features file into tab separated version, and delete the leftmost

Sep 27

qingyang feng, Ted Liefeld2

Sep 26

Error in GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

unread,

Error in GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

Sep 26

Jialing Gao, Ted Liefeld2

Sep 24

Error in GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

unread,

Error in GISTIC2.0

Hi There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be

Sep 24

Ananta Kapoor, Andrew Cherniack3

Sep 23

CNV using GISTIC

Sir I will read more thankyou. Please confirm this. On Thursday, September 14, 2023 at 12:46:53 AM

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CNV using GISTIC

Sir I will read more thankyou. Please confirm this. On Thursday, September 14, 2023 at 12:46:53 AM

Sep 23

Güllü Elif Özdemir, … Andrew Cherniack26

Sep 20

NO RESULT FOR GISTIC2.0

This is not the correct input file for GISTIC. It should be a .seg file that looks like this. https:/

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NO RESULT FOR GISTIC2.0

This is not the correct input file for GISTIC. It should be a .seg file that looks like this. https:/

Sep 20

Prit Benny, … shahin rmz3

Sep 19

3 Years later... Thank you Barbara. On Tuesday, May 12, 2020 at 12:32:35 AM UTC+2 Barbara Hill wrote:

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3 Years later... Thank you Barbara. On Tuesday, May 12, 2020 at 12:32:35 AM UTC+2 Barbara Hill wrote:

Sep 19

shahin rmz, Ted Liefeld3

Sep 19

Noob Errors with GISTIC2

Tried once again, and it works like charm. Thanks!! On Tuesday, September 19, 2023 at 4:11:13 PM UTC+

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Noob Errors with GISTIC2

Tried once again, and it works like charm. Thanks!! On Tuesday, September 19, 2023 at 4:11:13 PM UTC+

Sep 19

David Waneback, Anthony Castanza4

Sep 7

Gene signature from cell lines sensitivity screens

Hi David, For two-phenotype GSEA you're correct that we would not recommend using TPM data,

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Gene signature from cell lines sensitivity screens

Hi David, For two-phenotype GSEA you're correct that we would not recommend using TPM data,

Sep 7

fz z, Ted Liefeld2

Sep 5

Error in SubMap

Hi per the contents of the stderr file, the job simply did not have enough memory assigned. I reran

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Error in SubMap

Hi per the contents of the stderr file, the job simply did not have enough memory assigned. I reran

Sep 5

HT Liu, Ted Liefeld3

Sep 1

Seeking help for error in MutSigCV

All right. I will have a try on GATK forum. Thanks a lot! 在2023年9月1日星期五 UTC+8 00:50:03<Ted Liefeld

unread,

Seeking help for error in MutSigCV

All right. I will have a try on GATK forum. Thanks a lot! 在2023年9月1日星期五 UTC+8 00:50:03<Ted Liefeld

Sep 1

Abraam Zakhary, Ted Liefeld2

Aug 31

Error in hierarchical clustering

Hi, it appears (via testing) the HierarchicalClustering module requires the ".gct" file

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Error in hierarchical clustering

Hi, it appears (via testing) the HierarchicalClustering module requires the ".gct" file

Aug 31

Sakshi sen, Ted Liefeld7

Aug 15

ERR in MutSigCV

That documentation dates back about 10 years ago so its not too surprising the link no longer works.

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ERR in MutSigCV

That documentation dates back about 10 years ago so its not too surprising the link no longer works.

Aug 15

Sakshi sen, Ted Liefeld2

Aug 14

ERR in coverage file of MutSigcv

Hi I am unaware of any tools to automatically generate the file. It is a tab-delimited format and the

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ERR in coverage file of MutSigcv

Hi I am unaware of any tools to automatically generate the file. It is a tab-delimited format and the

Aug 14

Stephane Plaisance, Ted Liefeld3

Aug 11

reset user password without mail service

I am glad you figured out a path through. For future reference here is what I would have suggested 0.

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reset user password without mail service

I am glad you figured out a path through. For future reference here is what I would have suggested 0.

Aug 11

Ted Liefeld, Rashid O4

Aug 9

Re: [genepattern-help:2790] Issue with mounting jobResults folder

Hi It sounds like the machine you are using just does not have enough ram and CPU. It sounds like the

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Re: [genepattern-help:2790] Issue with mounting jobResults folder

Hi It sounds like the machine you are using just does not have enough ram and CPU. It sounds like the

Aug 9

Güllü Elif Özdemir, Ted Liefeld5

Aug 8

Of course. Thank you again. I wish you good work. 8 Ağustos 2023 Salı tarihinde Ted Liefeld <

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Of course. Thank you again. I wish you good work. 8 Ağustos 2023 Salı tarihinde Ted Liefeld <

Aug 8

Güllü Elif Özdemir, Andrew Cherniack2

Aug 1

Hi Gullu, Can you send the error message in the output and your seg file? Regards, Andrew Cherniack

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Hi Gullu, Can you send the error message in the output and your seg file? Regards, Andrew Cherniack

Aug 1

Sam, Ted Liefeld2

Jul 25

Error in PTM-SEA

Hi It looks like you used a github link for the gmt file. That results in the module downloading the

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Error in PTM-SEA

Hi It looks like you used a github link for the gmt file. That results in the module downloading the

Jul 25

Crane Tiger, Ted Liefeld4

Jul 25

Xinchen, a new version (6) of NearestTemplatePrediction has been released and it no longer has this

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Xinchen, a new version (6) of NearestTemplatePrediction has been released and it no longer has this

Jul 25

aswanikri...@gmail.com, edh...@cloud.ucsd.edu5

Jul 18

DEseq2 Error with HTSeq counts

Hi Edwin, Thank you so much for the help. -- Thanks & Regards Aswani Krishna.P On Mon, Jul 17,

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DEseq2 Error with HTSeq counts

Hi Edwin, Thank you so much for the help. -- Thanks & Regards Aswani Krishna.P On Mon, Jul 17,

Jul 18

Matin Salehi, tmt...@cloud.ucsd.edu2

Jul 10

Gistic arm-level vs focal-level

Hello, Can you provide a job number and I will take a look? However, it might be best to ask this

unread,

Gistic arm-level vs focal-level

Hello, Can you provide a job number and I will take a look? However, it might be best to ask this

Jul 10

Atsuyuki Kishibe, Ted Liefeld5

Jul 6

Error when using SubMap module

Hi Ted, Thanks for pointing out these issues, and I also successfully ran the module and got the

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Error when using SubMap module

Hi Ted, Thanks for pointing out these issues, and I also successfully ran the module and got the

Jul 6

Jul 1

incorrect number of data points error

ok i figured it out. basically should let the "preprocess and utilities" make the .cls file

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incorrect number of data points error

ok i figured it out. basically should let the "preprocess and utilities" make the .cls file

Jul 1

Rashid O, … Ted Liefeld11

Jun 27

Error when running module self hosted server

Yes - I'm able to use modules perfectly and jobs aren't causing any errors - Thanks as always

unread,

Error when running module self hosted server

Yes - I'm able to use modules perfectly and jobs aren't causing any errors - Thanks as always

Jun 27

JUNXI FENG, tmt...@cloud.ucsd.edu2

Jun 27

Error with ExpressionFileCreator

Hello, Could you please send the job number of the job with the error, this way I can look at the

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Error with ExpressionFileCreator

Hello, Could you please send the job number of the job with the error, this way I can look at the

Jun 27

Matin Salehi, Thorin Tabor3

Jun 22

Gistic public server doesn't work

Dear Thorin, Many thanks for your response. I tried today and it is working again. But I had problem

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Gistic public server doesn't work

Dear Thorin, Many thanks for your response. I tried today and it is working again. But I had problem

Jun 22

David Venet, … Alison Taylor7

Jun 16

That worked fo rme! Thanks so much for your help On Thursday, June 15, 2023 at 7:36:36 PM UTC-4 Ted

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That worked fo rme! Thanks so much for your help On Thursday, June 15, 2023 at 7:36:36 PM UTC-4 Ted

Jun 16

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