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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
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.
Happy posting!
-The GenePattern team
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Roser Pinyol
,
Ted Liefeld
4
Jul 25
ssGSEA says "Task failed to start"
Roser the changes have been made. Please re-submit your jobs and let me know how it goes. I tried to
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ssGSEA says "Task failed to start"
Roser the changes have been made. Please re-submit your jobs and let me know how it goes. I tried to
Jul 25
Jihyun Youn
,
Anthony Castanza
2
Jul 24
Question regarding ssGSEA
Hi Jane, The general approach is just to fill it in with a zero. But ultimately it depends on why the
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Question regarding ssGSEA
Hi Jane, The general approach is just to fill it in with a zero. But ultimately it depends on why the
Jul 24
Debajyoti Kabiraj
, …
Andrew Cherniack
6
Jul 9
GISTIC_2.0 Error
Thanks for your valuable responses, after adding the header it's working. Best, Deb On Monday,
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GISTIC_2.0 Error
Thanks for your valuable responses, after adding the header it's working. Best, Deb On Monday,
Jul 9
Mohammed Noor
,
edh...@cloud.ucsd.edu
5
Jul 8
Error Encountered While Running ssGSEA on GenePattern
Hi Ariyan, The issue is that you have ~3420 genes in the gene set that you provided, however ssGSEA
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Error Encountered While Running ssGSEA on GenePattern
Hi Ariyan, The issue is that you have ~3420 genes in the gene set that you provided, however ssGSEA
Jul 8
Eunice lly
, …
Andrew Cherniack
15
Jul 1
GISTIC2.0 Floating point exception error
Hi Andrew, Thank you for the prompt response. Yes, I rerun it recently and same error occurred. My
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GISTIC2.0 Floating point exception error
Hi Andrew, Thank you for the prompt response. Yes, I rerun it recently and same error occurred. My
Jul 1
Ted Liefeld
Jun 27
Re: [genepattern-help:3034] Re: DeSeq2 job error RNAseq Raw readcount
Hi, In future, please send your help requests to the GenePattern help forum, https://groups.google.
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Re: [genepattern-help:3034] Re: DeSeq2 job error RNAseq Raw readcount
Hi, In future, please send your help requests to the GenePattern help forum, https://groups.google.
Jun 27
Teresa Harris
,
Ted Liefeld
3
Jun 24
GISTIC 2.0 No output, Job processing for multiple hours
Hi again, we think we know the proximal cause of the failure, but it will take a bit of time before a
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GISTIC 2.0 No output, Job processing for multiple hours
Hi again, we think we know the proximal cause of the failure, but it will take a bit of time before a
Jun 24
Hossein Valipour Kahrood
,
Thorin Tabor
5
Jun 10
VisualizerLauncher
Hi Thorin, Thanks for the clarification. Regards, Hossein On Tue, 11 Jun 2024 at 02:30, Thorin Tabor
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VisualizerLauncher
Hi Thorin, Thanks for the clarification. Regards, Hossein On Tue, 11 Jun 2024 at 02:30, Thorin Tabor
Jun 10
bri colletti
,
forre...@gmail.com
2
May 31
Job Run Error
Hi Bri, Sorry you are having issues with the tool. Can you send us the GenePattern job id so we can
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Job Run Error
Hi Bri, Sorry you are having issues with the tool. Can you send us the GenePattern job id so we can
May 31
stella
May 11
[GISTIC2.0] Floating point exception
Dear Gene Pattern team, Hi, I'm a Gene Pattern User. When I run the GISTIC 2.0, I got this error,
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[GISTIC2.0] Floating point exception
Dear Gene Pattern team, Hi, I'm a Gene Pattern User. When I run the GISTIC 2.0, I got this error,
May 11
Roser Pinyol
,
Ted Liefeld
4
May 9
sub-directory
Many thanks!! Best wishes Roser Missatge de 'Ted Liefeld' via GenePattern Help Forum <
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sub-directory
Many thanks!! Best wishes Roser Missatge de 'Ted Liefeld' via GenePattern Help Forum <
May 9
Roser Pinyol
,
Ted Liefeld
2
May 9
sub-directory re-name function does not work
Hi, I responded to this in your other help request. Ted On Wednesday, May 8, 2024 at 10:46:47 PM UTC-
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sub-directory re-name function does not work
Hi, I responded to this in your other help request. Ted On Wednesday, May 8, 2024 at 10:46:47 PM UTC-
May 9
ravi
,
forre...@gmail.com
6
May 7
TargetedDNASeq_VCF to MAF and downstream analysis
Thank you, Forrest. On Tue, 7 May 2024 at 03:50, forre...@gmail.com <forre...@gmail.com>
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TargetedDNASeq_VCF to MAF and downstream analysis
Thank you, Forrest. On Tue, 7 May 2024 at 03:50, forre...@gmail.com <forre...@gmail.com>
May 7
Angelussong
,
Ted Liefeld
6
Apr 30
MutsigCV job got terminated
The job finished without any error. Thanks so much for your help! On Tue, Apr 30, 2024 at 10:39 AM
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MutsigCV job got terminated
The job finished without any error. Thanks so much for your help! On Tue, Apr 30, 2024 at 10:39 AM
Apr 30
Abraam Zakhary
,
edh...@cloud.ucsd.edu
3
Apr 30
MutSigCV help
Hi Abraam, Sorry for the late reply. What was your job ID for the run? Edwin On Tuesday, April 30,
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MutSigCV help
Hi Abraam, Sorry for the late reply. What was your job ID for the run? Edwin On Tuesday, April 30,
Apr 30
Daniel Fisher
,
edh...@cloud.ucsd.edu
5
Apr 29
TCGA gene set query
Hi Edwin, Thank you! I'll read the guide you sent and then try it. If I have any problems, I'
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TCGA gene set query
Hi Edwin, Thank you! I'll read the guide you sent and then try it. If I have any problems, I'
Apr 29
Gabriel Mesa
,
Anthony Castanza
7
Apr 26
ssGSEA Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed
I really appreciate your help thank you so much. Have a great day, Gabriel Mesa On Thursday, April 25
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ssGSEA Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed
I really appreciate your help thank you so much. Have a great day, Gabriel Mesa On Thursday, April 25
Apr 26
Yun Xiao
,
Andrew Cherniack
2
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 Liefeld
2
Apr 15
NTP
There seems to be an issue between the GenePattern server and the compute nodes that the jobs are
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NTP
There seems to be an issue between the GenePattern server and the compute nodes that the jobs are
Apr 15
Karen Ross
, …
Felix Geist
7
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 Castanza
5
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 Несмелов
5
Apr 10
Q&A
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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Q&A
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 Liefeld
6
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 Liefeld
7
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 Cherniack
13
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 Liefeld
3
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 Liefeld
5
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 Liefeld
4
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
unread,
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 Castanza
3
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
unread,
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 Liefeld
11
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