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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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Joan Slonczewski
,
Ted Liefeld
8
Aug 12
FCS to CSV
I am glad that things are working for you now. Let us know if you have any other questions Ted On Fri
unread,
FCS to CSV
I am glad that things are working for you now. Let us know if you have any other questions Ted On Fri
Aug 12
Maria K
, …
Alex Wenzel
7
Aug 10
Upload of data
That could be very useful!! I will check this! Thanks you so much Alex!! Best wishes, Maria Στις Τετ,
unread,
Upload of data
That could be very useful!! I will check this! Thanks you so much Alex!! Best wishes, Maria Στις Τετ,
Aug 10
sot
,
Ted Liefeld
9
Aug 4
error using module TCGAImporter
Thanks! :-) Στις Τετάρτη 3 Αυγούστου 2022 στις 9:13:22 μ.μ. UTC+3, ο χρήστης lie...@broadinstitute.
unread,
error using module TCGAImporter
Thanks! :-) Στις Τετάρτη 3 Αυγούστου 2022 στις 9:13:22 μ.μ. UTC+3, ο χρήστης lie...@broadinstitute.
Aug 4
Sruthi S
,
mmr...@cloud.ucsd.edu
5
Jul 22
Multiplot studio
Ok, thank you!! I tried and it worked! Sruthi Mailtrack Sender notified by Mailtrack 07/23/22, 02:21:
unread,
Multiplot studio
Ok, thank you!! I tried and it worked! Sruthi Mailtrack Sender notified by Mailtrack 07/23/22, 02:21:
Jul 22
Julia Huguet
,
forre...@gmail.com
2
Jul 21
ssGSEA error
Hi Júlia, Can you tell me a bit about where you are connecting from (geographically and the
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ssGSEA error
Hi Júlia, Can you tell me a bit about where you are connecting from (geographically and the
Jul 21
vineelaga...@gmail.com
,
Anthony Castanza
2
Jul 21
ssGSEA error
Hello, So at least part of the issue here is that ssGSEA has an internally hard-coded maximum gene
unread,
ssGSEA error
Hello, So at least part of the issue here is that ssGSEA has an internally hard-coded maximum gene
Jul 21
Yuqin Feng
,
Anthony Castanza
5
Jul 12
ssGSEA error
Hello again, One of my colleagues pointed out that there are still potentially issues with the gmx
unread,
ssGSEA error
Hello again, One of my colleagues pointed out that there are still potentially issues with the gmx
Jul 12
Amphun chaiboonchoe
, …
Ted Liefeld
8
Jul 12
Submap error
Hi again. We have released a new version of SubMap (4.0) and it is now available on our public server
unread,
Submap error
Hi again. We have released a new version of SubMap (4.0) and it is now available on our public server
Jul 12
Kathrin Julia Laue
,
Anthony Castanza
2
Jul 4
how to generate GSEA plots with ssGSEA?
Hi Kathrin, Unfortunately the ssGSEA module does not produce an analogue of the traditional GSEA
unread,
how to generate GSEA plots with ssGSEA?
Hi Kathrin, Unfortunately the ssGSEA module does not produce an analogue of the traditional GSEA
Jul 4
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
unread,
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
unread,
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
unread,
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
unread,
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
unread,
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
unread,
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-
unread,
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
unread,
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
unread,
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
unread,
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
unread,
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
unread,
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.
unread,
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
unread,
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!
unread,
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
unread,
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
unread,
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
unread,
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
unread,
Error in ssGSEA
Hi, Anthony Thank you very much for your help. I have just successfully done the ssGSEA by changing
Mar 31