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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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sunand...@gmail.com
,
Ted Liefeld
2
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 Liefeld
4
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
unread,
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 Eby
4
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.edu
9
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 Azari
9
Feb 14
GISTIC2 Issue
thanks for your reply thorin 🌹 On Tue, Feb 14, 2023, 10:23 PM tmt...@cloud.ucsd.edu <tmtabor@cloud
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GISTIC2 Issue
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.edu
3
Feb 13
GISTIC issue
We have just updated the GISTIC_2.0 module. Please try again. Thorin Tabor GenePattern Team On Monday
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GISTIC issue
We have just updated the GISTIC_2.0 module. Please try again. Thorin Tabor GenePattern Team On Monday
Feb 13
Mingyuan Wan
, …
Ted Liefeld
6
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 Azari
4
Feb 13
Q&A
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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Q&A
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 SASSI
12
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 Liefeld
3
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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Error
Gistic
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.edu
3
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 Liefeld
4
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 Reich
2
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.edu
2
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 Castanza
9
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 Liefeld
2
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 Liefeld
4
11/28/22
Q&A
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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Q&A
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.edu
2
11/21/22
scRNA analysis
Hello Sruthi, We will add this as a feature request, but unfortunately Mutiplot Studio does not
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scRNA analysis
Hello Sruthi, We will add this as a feature request, but unfortunately Mutiplot Studio does not
11/21/22
Neelam Shinde
, …
Anthony Castanza
8
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 Liefeld
4
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 Liefeld
3
11/9/22
MutsigCV error
Thank you, Ted. I will contact the google group you have referenced. Sumithra On Mon, Nov 7, 2022 at
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MutsigCV error
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 Liefeld
6
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 Liefeld
3
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 Liefeld
7
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 Castanza
7
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 Tabor
5
10/25/22
FLAME modules
Hello, You can find the source for the FLAME modules at the following links: FlamePreprocess: https:/
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FLAME modules
Hello, You can find the source for the FLAME modules at the following links: FlamePreprocess: https:/
10/25/22
Mario Ezquerra
,
Anthony Castanza
3
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 Liefeld
3
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 Castanza
3
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
unread,
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 Castanza
8
10/18/22
ssGSEA error
Hi Jaishree, To follow up Ted's answer, the results in the .PROJ.gct file are the enrichment
unread,
ssGSEA error
Hi Jaishree, To follow up Ted's answer, the results in the .PROJ.gct file are the enrichment
10/18/22