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.

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Happy posting!

-The GenePattern team

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Joan Slonczewski, Ted Liefeld8

Aug 12

I am glad that things are working for you now. Let us know if you have any other questions Ted On Fri

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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 Wenzel7

Aug 10

That could be very useful!! I will check this! Thanks you so much Alex!! Best wishes, Maria Στις Τετ,

unread,

That could be very useful!! I will check this! Thanks you so much Alex!! Best wishes, Maria Στις Τετ,

Aug 10

sot, Ted Liefeld9

Aug 4

error using module TCGAImporter

Thanks! :-) Στις Τετάρτη 3 Αυγούστου 2022 στις 9:13:22 μ.μ. UTC+3, ο χρήστης lie...@broadinstitute.

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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.edu5

Jul 22

Multiplot studio

Ok, thank you!! I tried and it worked! Sruthi Mailtrack Sender notified by Mailtrack 07/23/22, 02:21:

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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.com2

Jul 21

Hi Júlia, Can you tell me a bit about where you are connecting from (geographically and the

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Hi Júlia, Can you tell me a bit about where you are connecting from (geographically and the

Jul 21

vineelaga...@gmail.com, Anthony Castanza2

Jul 21

Hello, So at least part of the issue here is that ssGSEA has an internally hard-coded maximum gene

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Hello, So at least part of the issue here is that ssGSEA has an internally hard-coded maximum gene

Jul 21

Yuqin Feng, Anthony Castanza5

Jul 12

Hello again, One of my colleagues pointed out that there are still potentially issues with the gmx

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Hello again, One of my colleagues pointed out that there are still potentially issues with the gmx

Jul 12

Amphun chaiboonchoe, … Ted Liefeld8

Jul 12

Hi again. We have released a new version of SubMap (4.0) and it is now available on our public server

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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 Castanza2

Jul 4

how to generate GSEA plots with ssGSEA?

Hi Kathrin, Unfortunately the ssGSEA module does not produce an analogue of the traditional GSEA

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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 Liefeld5

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 Liefeld4

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 Liefeld3

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 Haefliger2

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.edu7

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

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 Liefeld2

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 Castanza3

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.edu2

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 Castanza10

Apr 28

Hello, The actual issue here appears to be something related to the container exiting. This can occur

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Hello, The actual issue here appears to be something related to the container exiting. This can occur

Apr 28

Alkaid, … Anthony Castanza12

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

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 Liefeld4

Apr 25

Elvin, what is your username and where (geographically) are you connecting from? The 403 error is a

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Elvin, what is your username and where (geographically) are you connecting from? The 403 error is a

Apr 25

Donna Bedasee, Anthony Castanza2

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 Castanza15

Apr 21

Hello, I wasn't able to view your job ID directly, because it appears that that job was deleted.

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Hello, I wasn't able to view your job ID directly, because it appears that that job was deleted.

Apr 21

Geraint Xia, Ted Liefeld2

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 Allen5

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 Castanza3

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 Castanza2

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 Castanza3

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

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