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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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Fan Ge
,
Ted Liefeld
2
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
unread,
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 Cherniack
7
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-
unread,
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
unread,
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 Liefeld
3
Sep 27
Trouble with NTP(nearest template prediction)
Thanks After I change the input.features file into tab separated version, and delete the leftmost
unread,
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 Liefeld
2
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 Liefeld
2
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 Cherniack
3
Sep 23
CNV using GISTIC
Sir I will read more thankyou. Please confirm this. On Thursday, September 14, 2023 at 12:46:53 AM
unread,
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 Cherniack
26
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:/
unread,
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 rmz
3
Sep 19
Q&A
GISTIC plots
3 Years later... Thank you Barbara. On Tuesday, May 12, 2020 at 12:32:35 AM UTC+2 Barbara Hill wrote:
unread,
Q&A
GISTIC plots
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 Liefeld
3
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+
unread,
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 Castanza
4
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,
unread,
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 Liefeld
2
Sep 5
Error in SubMap
Hi per the contents of the stderr file, the job simply did not have enough memory assigned. I reran
unread,
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 Liefeld
3
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 Liefeld
2
Aug 31
Error in hierarchical clustering
Hi, it appears (via testing) the HierarchicalClustering module requires the ".gct" file
unread,
Error in hierarchical clustering
Hi, it appears (via testing) the HierarchicalClustering module requires the ".gct" file
Aug 31
Sakshi sen
,
Ted Liefeld
7
Aug 15
ERR in MutSigCV
That documentation dates back about 10 years ago so its not too surprising the link no longer works.
unread,
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 Liefeld
2
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
unread,
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 Liefeld
3
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.
unread,
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 O
4
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
unread,
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 Liefeld
5
Aug 8
SubMap
Of course. Thank you again. I wish you good work. 8 Ağustos 2023 Salı tarihinde Ted Liefeld <
unread,
SubMap
Of course. Thank you again. I wish you good work. 8 Ağustos 2023 Salı tarihinde Ted Liefeld <
Aug 8
Güllü Elif Özdemir
,
Andrew Cherniack
2
Aug 1
Error
Hi Gullu, Can you send the error message in the output and your seg file? Regards, Andrew Cherniack
unread,
Error
Hi Gullu, Can you send the error message in the output and your seg file? Regards, Andrew Cherniack
Aug 1
Sam
,
Ted Liefeld
2
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
unread,
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 Liefeld
4
Jul 25
Error in NTP
Xinchen, a new version (6) of NearestTemplatePrediction has been released and it no longer has this
unread,
Error in NTP
Xinchen, a new version (6) of NearestTemplatePrediction has been released and it no longer has this
Jul 25
aswanikri...@gmail.com
,
edh...@cloud.ucsd.edu
5
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,
unread,
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.edu
2
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 Liefeld
5
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
unread,
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
Wayne
2
Jul 1
incorrect number of data points error
ok i figured it out. basically should let the "preprocess and utilities" make the .cls file
unread,
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 Liefeld
11
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.edu
2
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
unread,
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 Tabor
3
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
unread,
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 Taylor
7
Jun 16
GISTIC error
That worked fo rme! Thanks so much for your help On Thursday, June 15, 2023 at 7:36:36 PM UTC-4 Ted
unread,
GISTIC error
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