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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
Facebook
and
Twitter
.
Happy posting!
-The GenePattern team
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Yuqin Feng
Jul 3
ssGSEA error
Hello everyone, I just tried "ssGSEA" with uploaded gene list GMX file. Job Number:448296.
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ssGSEA error
Hello everyone, I just tried "ssGSEA" with uploaded gene list GMX file. Job Number:448296.
Jul 3
Amphun chaiboonchoe
Jun 30
Submap error
Hi I have an error ' memory not mapped' while using the Submap module. *** caught segfault **
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Submap error
Hi I have an error ' memory not mapped' while using the Submap module. *** caught segfault **
Jun 30
Patricia Mingo
,
Ted Liefeld
5
Jun 24
DESeq2 troubles
Hi Ted, Thanks for your message! Hope it works know Patricia El viernes, 24 de junio de 2022 a las 20
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DESeq2 troubles
Hi Ted, Thanks for your message! Hope it works know Patricia El viernes, 24 de junio de 2022 a las 20
Jun 24
Sruthi S
,
Ted Liefeld
4
Jun 24
Error in DESeq2
Hi We have just deployed a new container for the DESeq2 module and we believe it should be working
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Error in DESeq2
Hi We have just deployed a new container for the DESeq2 module and we believe it should be working
Jun 24
Shwetha Kumar
,
Ted Liefeld
3
Jun 22
Job ID 446023 and Job ID446027
Thank you so much. Shwetha On Wed, Jun 22, 2022 at 12:43 PM Ted Liefeld <liefeld@broadinstitute.
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Job ID 446023 and Job ID446027
Thank you so much. Shwetha On Wed, Jun 22, 2022 at 12:43 PM Ted Liefeld <liefeld@broadinstitute.
Jun 22
Simon Haefliger
2
Jun 10
MethylationCNVAnalysis v2.4
Hi The job number for the request below is 444014. Thanks for your help Best regards Simon ----------
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MethylationCNVAnalysis v2.4
Hi The job number for the request below is 444014. Thanks for your help Best regards Simon ----------
Jun 10
二哈李
,
tmt...@cloud.ucsd.edu
7
Jun 9
Trouble with NearestTemplatePrediction
Hello, It's really a problem with the file encoding. After modifying the file encoding, the
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Trouble with NearestTemplatePrediction
Hello, It's really a problem with the file encoding. After modifying the file encoding, the
Jun 9
Ted Liefeld
May 27
Re: [gp-help-no-reply] Question request
Hi The problem is simply that your job exceeded the default 2-hour time limit for the job. Try
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Re: [gp-help-no-reply] Question request
Hi The problem is simply that your job exceeded the default 2-hour time limit for the job. Try
May 27
Mauricio Cuello
,
Ted Liefeld
2
May 23
Trouble with DESeq2
Hi DESeq2 should be working again now, we are sorry for the inconvenience. The problem was that for a
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Trouble with DESeq2
Hi DESeq2 should be working again now, we are sorry for the inconvenience. The problem was that for a
May 23
Hai Tran
,
Anthony Castanza
3
May 16
error ssGSEA.ROC
Dear Anthony, Thank you very much for your quick response and help. The version in clound you
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error ssGSEA.ROC
Dear Anthony, Thank you very much for your quick response and help. The version in clound you
May 16
Josephine Klitgaard
,
mmr...@cloud.ucsd.edu
2
May 6
Comparative marker selection on rpm-plus1log2 Ion Torrent RNAseq data
Hi Josephine, Apologies for the delayed response. Because of the distribution assumptions of the T-
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Comparative marker selection on rpm-plus1log2 Ion Torrent RNAseq data
Hi Josephine, Apologies for the delayed response. Because of the distribution assumptions of the T-
May 6
Baharia Mograbi
, …
Anthony Castanza
10
Apr 28
ssGSEA failled
Hello, The actual issue here appears to be something related to the container exiting. This can occur
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ssGSEA failled
Hello, The actual issue here appears to be something related to the container exiting. This can occur
Apr 28
Alkaid
, …
Anthony Castanza
12
Apr 27
invalid multibyte string-ssGSEA
My apologies, I sent my reply too soon, ssGSEA has an internal gene set size limit of 2000 genes. I
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invalid multibyte string-ssGSEA
My apologies, I sent my reply too soon, ssGSEA has an internal gene set size limit of 2000 genes. I
Apr 27
Ted Liefeld
Apr 27
Re: [gp-team] I am curious about the licensing policy.
Hi GenePattern is free to use for all users. If you wish to set up your own server, our open source
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Re: [gp-team] I am curious about the licensing policy.
Hi GenePattern is free to use for all users. If you wish to set up your own server, our open source
Apr 27
Elvin Yang
,
Ted Liefeld
4
Apr 25
ssGSEA error
Elvin, what is your username and where (geographically) are you connecting from? The 403 error is a
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ssGSEA error
Elvin, what is your username and where (geographically) are you connecting from? The 403 error is a
Apr 25
Donna Bedasee
,
Anthony Castanza
2
Apr 22
new to genepattern; help with errors
Hello, Unfortunately it appears you deleted the errored job, we can't provide detailed debugging
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new to genepattern; help with errors
Hello, Unfortunately it appears you deleted the errored job, we can't provide detailed debugging
Apr 22
Mohamed Kamal
, …
Anthony Castanza
15
Apr 21
ssGSEA
Hello, I wasn't able to view your job ID directly, because it appears that that job was deleted.
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ssGSEA
Hello, I wasn't able to view your job ID directly, because it appears that that job was deleted.
Apr 21
Geraint Xia
,
Ted Liefeld
2
Apr 15
GISTIC2 CNV Analysis
Hi this was due to a bug in job delegation that affected about 10% of GISTIC jobs over the last few
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GISTIC2 CNV Analysis
Hi this was due to a bug in job delegation that affected about 10% of GISTIC jobs over the last few
Apr 15
Joe Allen
, …
Joe Allen
5
Apr 12
Unexpected Error after Importing GCT in GSEA
Hi Anthony, I think I figured it out! Just a formatting issue in my GCT. Thanks for all of your help!
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Unexpected Error after Importing GCT in GSEA
Hi Anthony, I think I figured it out! Just a formatting issue in my GCT. Thanks for all of your help!
Apr 12
Sara Balch
,
Anthony Castanza
3
Apr 4
ssGSEA gene set file error
Thank you for such a quick response and for finding a solution! I appreciate all the help! Sara On
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ssGSEA gene set file error
Thank you for such a quick response and for finding a solution! I appreciate all the help! Sara On
Apr 4
GenePattern Help Forum
Mar 31
Announcement: Salmon.Indexer & Salmon.Quant updated to use Salmon 1.6.0
Salmon.Quant & Salmon.Indexer have been updated to Salmon 1.6.0, and Quant now provides indices
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Announcement: Salmon.Indexer & Salmon.Quant updated to use Salmon 1.6.0
Salmon.Quant & Salmon.Indexer have been updated to Salmon 1.6.0, and Quant now provides indices
Mar 31
吳尚殷_Wu Shang-Yin
,
Anthony Castanza
2
Mar 31
Error in ComparativeMarkerSelection
Hi Shang-Yin, Desktop GSEA uses a slightly looser definition of the CLS file specification than
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Error in ComparativeMarkerSelection
Hi Shang-Yin, Desktop GSEA uses a slightly looser definition of the CLS file specification than
Mar 31
Tak, Takuma Nakashima
,
Anthony Castanza
3
Mar 31
Error in ssGSEA
Hi, Anthony Thank you very much for your help. I have just successfully done the ssGSEA by changing
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Error in ssGSEA
Hi, Anthony Thank you very much for your help. I have just successfully done the ssGSEA by changing
Mar 31
Mouncef El Ouardi
,
Barbara Hill
4
Mar 30
Issue while installing DAPPLE on local genepattern server
Hello, I'm not sure why you building a new image. The published version of DAPPLE in our GParc
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DAPPLE
Issue while installing DAPPLE on local genepattern server
Hello, I'm not sure why you building a new image. The published version of DAPPLE in our GParc
Mar 30
daniel...@gmail.com
, …
Ted Liefeld
5
Mar 29
ssGSEA doesn't work
Thanks Ted, when I re-uploaded the signature file, everything worked perfectly. Thanks again, Daniel
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ssGSEA doesn't work
Thanks Ted, when I re-uploaded the signature file, everything worked perfectly. Thanks again, Daniel
Mar 29
Michelle Hulke
2
Mar 24
Error Running GSEApreranked
Never mind. It seems to be working now. On Thursday, March 24, 2022 at 3:48:52 PM UTC-4 Michelle
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Error Running GSEApreranked
Never mind. It seems to be working now. On Thursday, March 24, 2022 at 3:48:52 PM UTC-4 Michelle
Mar 24
孙强
,
Ted Liefeld
2
Mar 24
Gistic2 problems
Hi This can happen sometimes when demand on the GenePattern servers is high. Lately we have had
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Gistic2 problems
Hi This can happen sometimes when demand on the GenePattern servers is high. Lately we have had
Mar 24
Vithurran Thavarajah
,
Barbara Hill
2
Mar 14
Website down
Hello, GenePattern.org, the website where we host documentation about the server, was indeed down and
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Website down
Hello, GenePattern.org, the website where we host documentation about the server, was indeed down and
Mar 14
Yuta Ito
,
tmt...@cloud.ucsd.edu
2
Mar 7
【GISTIC result for chromosome X】
Hello Yuta, For an issue like this, it is best to post in the GISTIC Forum, where the lead developer
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【GISTIC result for chromosome X】
Hello Yuta, For an issue like this, it is best to post in the GISTIC Forum, where the lead developer
Mar 7
Elena Lara
,
Barbara Hill
3
Mar 2
Error in perform Ziggurat deconstruction
Thank you, Barbara. I moved the question to https://groups.google.com/a/broadinstitute.org/g/gistic-
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Error in perform Ziggurat deconstruction
Thank you, Barbara. I moved the question to https://groups.google.com/a/broadinstitute.org/g/gistic-
Mar 2