GenePattern Help Forum

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12:02 PM

ssGSEA Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed

Here is the job information as well: # Job: 577648 # User: ghm15 # Submitted: 2024-04-19 15:50:17.0 #

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ssGSEA Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed

Here is the job information as well: # Job: 577648 # User: ghm15 # Submitted: 2024-04-19 15:50:17.0 #

12:02 PM

Yun Xiao, Andrew Cherniack2

Apr 16

GICTIC Floating point exception

Can you provide more information? What were your input parameters? What was your segfile? On Sunday,

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GICTIC Floating point exception

Can you provide more information? What were your input parameters? What was your segfile? On Sunday,

Apr 16

Roser Pinyol, Ted Liefeld2

Apr 15

There seems to be an issue between the GenePattern server and the compute nodes that the jobs are

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There seems to be an issue between the GenePattern server and the compute nodes that the jobs are

Apr 15

Karen Ross, … Felix Geist7

Apr 11

Very Long Queue

Hi, thanks for your super fast reply!! I was really stunned by the number of jobs in the queue and as

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Very Long Queue

Hi, thanks for your super fast reply!! I was really stunned by the number of jobs in the queue and as

Apr 11

Kathy Ma, Anthony Castanza5

Apr 11

Question about ssGSEA and prerank usage

That's fine. Thank you so much for your help! Regards, Kathy Ma On Tue, Apr 9, 2024 at 1:33 PM

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Question about ssGSEA and prerank usage

That's fine. Thank you so much for your help! Regards, Kathy Ma On Tue, Apr 9, 2024 at 1:33 PM

Apr 11

pushpinde...@gmail.com, … Александр Несмелов5

Apr 10

MutSigCV coverage file

Yes, it works with this file! Thank you so much! четверг, 4 апреля 2024 г. в 19:25:46 UTC+4, Ted

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MutSigCV coverage file

Yes, it works with this file! Thank you so much! четверг, 4 апреля 2024 г. в 19:25:46 UTC+4, Ted

Apr 10

anjali bajpai, Ted Liefeld6

Mar 20

ProteoArray, upload large mzmxl file

Hi, You should just drag and drop it from your files tab to the input field, not provide it as a file

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ProteoArray, upload large mzmxl file

Hi, You should just drag and drop it from your files tab to the input field, not provide it as a file

Mar 20

Sehrish Kanwal, Ted Liefeld7

Mar 13

MutPanning alignment errors

Hi Ted, Thanks for getting back to me. I tried formatting the MAF file to the format described in the

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MutPanning alignment errors

Hi Ted, Thanks for getting back to me. I tried formatting the MAF file to the format described in the

Mar 13

Fernando RB, … Andrew Cherniack13

Mar 8

Issue running GISTIC_2.0 module

Version 6.15.30 is now working perfectly. Thank you very much for your help! El jueves, 7 de marzo de

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Issue running GISTIC_2.0 module

Version 6.15.30 is now working perfectly. Thank you very much for your help! El jueves, 7 de marzo de

Mar 8

Eric David Elass@UW.Edu, Ted Liefeld3

Mar 7

Gistic error (multiple) source?

Hi, I actually believe I may have resolved the error. I believe it was caused by creating from .seg

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Gistic error (multiple) source?

Hi, I actually believe I may have resolved the error. I believe it was caused by creating from .seg

Mar 7

Sreeja S, … Ted Liefeld5

Mar 7

Not getting deletion plots in GISTIC2 results

I think you are right, sorry if you spent much time on this On Thursday, March 7, 2024 at 9:50:10 AM

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Not getting deletion plots in GISTIC2 results

I think you are right, sorry if you spent much time on this On Thursday, March 7, 2024 at 9:50:10 AM

Mar 7

Nerea Herrera, Ted Liefeld4

Mar 6

Error: memory not mapped

Hi there seems to be 2 problems with your input file. First , while you have declared 16 columns and

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Error: memory not mapped

Hi there seems to be 2 problems with your input file. First , while you have declared 16 columns and

Mar 6

Catarina Marques, Anthony Castanza3

Mar 6

Error in rep("null", max.Ng * max.size.G) : invalid 'times' argument

Hi Anthony, It worked! Thank you so much for your help, I really appreciate it! Cheers, Catarina On

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Error in rep("null", max.Ng * max.size.G) : invalid 'times' argument

Hi Anthony, It worked! Thank you so much for your help, I really appreciate it! Cheers, Catarina On

Mar 6

Nicolas Poux, … Ted Liefeld11

Feb 21

SNPFileCreator and CopyNumberInference

Nico I think those classes can be found in the jar file gp-module.jar. I have put a copy of that here

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SNPFileCreator and CopyNumberInference

Nico I think those classes can be found in the jar file gp-module.jar. I have put a copy of that here

Feb 21

Angelussong, Ted Liefeld3

Jan 29

Error running Gistic2

Thank you so much!! I'll test it now! On Mon, Jan 29, 2024 at 9:11 AM Ted Liefeld <liefeld@

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Error running Gistic2

Thank you so much!! I'll test it now! On Mon, Jan 29, 2024 at 9:11 AM Ted Liefeld <liefeld@

Jan 29

Gary Zhu, … Andrew Cherniack13

Jan 9

missing files in results.

Are you getting the same error message? ___________________________ Andrew Cherniack, PhD Senior

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missing files in results.

Are you getting the same error message? ___________________________ Andrew Cherniack, PhD Senior

Jan 9

Minu Seong, edh...@cloud.ucsd.edu3

Jan 5

Hi, For Salmon/Sailfish/Kallisto data providing the transcriptome file used to quantify the data is

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Hi, For Salmon/Sailfish/Kallisto data providing the transcriptome file used to quantify the data is

Jan 5

Andy Scherer, Michael Reich3

12/23/23

KNNX versus PCA

Thank you so much, Michael. The "interesting" aspect is though, that from the same study

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KNNX versus PCA

Thank you so much, Michael. The "interesting" aspect is though, that from the same study

12/23/23

Anne Van Arsdale, … edh...@cloud.ucsd.edu7

12/20/23

Hi, From the job results, I think your job result ID is 21657. I've recently replaced the mosek

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Hi, From the job results, I think your job result ID is 21657. I've recently replaced the mosek

12/20/23

Anna Fedenko, Ted Liefeld4

12/18/23

Server error running gistic_2

Hi Ted, Many thanks for your help, it seems to be working now :) Best wishes Anna On Fri, Dec 15,

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Server error running gistic_2

Hi Ted, Many thanks for your help, it seems to be working now :) Best wishes Anna On Fri, Dec 15,

12/18/23

Daniel Lee, Michael Reich3

11/27/23

ARACNE help please?

Dear Michael and all, Thanks for the answers. Do you agree with the boldened summaries below: Do I

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ARACNE help please?

Dear Michael and all, Thanks for the answers. Do you agree with the boldened summaries below: Do I

11/27/23

Praveen Raj, Ted Liefeld8

11/14/23

Error while installing module - can't get TaskInfo

Hi Ted I am using MySQL v8.0.32 on Alma Linux 9. EL9 does not support MySQL 5.7 though there is some

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Error while installing module - can't get TaskInfo

Hi Ted I am using MySQL v8.0.32 on Alma Linux 9. EL9 does not support MySQL 5.7 though there is some

11/14/23

yiqing zhang, Andrew Cherniack8

11/4/23

gistic2.0.23 error:Index exceeds matrix dimensions. Error in normalize_by_arm_length

One more thing. One more indication that there is something wrong with CN data is that you have

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gistic2.0.23 error:Index exceeds matrix dimensions. Error in normalize_by_arm_length

One more thing. One more indication that there is something wrong with CN data is that you have

11/4/23

11/2/23

Re: [gp-team] Re: Calling for deleting account

Hi I have removed your email and password from the account. Your user_id will remain but will be

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Re: [gp-team] Re: Calling for deleting account

Hi I have removed your email and password from the account. Your user_id will remain but will be

11/2/23

Caterina Colón

11/1/23

gistic non-human reference

Hello, are there any pointers to generating a non-human reference genome file to run on GISTIC? I

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gistic non-human reference

Hello, are there any pointers to generating a non-human reference genome file to run on GISTIC? I

11/1/23

yulu shi, Ted Liefeld2

10/18/23

NTP not work well

Hi There was a problem with the remote compute nodes that we use to execute NearestTemplatePrediction

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NTP not work well

Hi There was a problem with the remote compute nodes that we use to execute NearestTemplatePrediction

10/18/23

soogus, Ted Liefeld2

10/10/23

GenePattern GISTIC_2.0 Result error

Hi, when you see a result or error, you should always read the stdout and stderr files that are

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GenePattern GISTIC_2.0 Result error

Hi, when you see a result or error, you should always read the stdout and stderr files that are

10/10/23

Xiaofan Lu, Ted Liefeld2

10/9/23

Parameters used in my previous Job 526322

Hi, I have emailed the parameters to the email associated with the GenePattern account that ran this

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Parameters used in my previous Job 526322

Hi, I have emailed the parameters to the email associated with the GenePattern account that ran this

10/9/23

Sumithra Sankararaman, Andrew Cherniack2

10/6/23

units of copy-number in GISTIC

It's change in copy number from the baseline CN state of the tumor. In a diploid cell that would

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units of copy-number in GISTIC

It's change in copy number from the baseline CN state of the tumor. In a diploid cell that would

10/6/23

Fan Ge, Ted Liefeld2

10/2/23

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

10/2/23

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