Error when building enrichment map

[ghost]

Hi,
in module 3 lab exercise 2 when building enrichment map I always get error 'No genes in the expression file are found in the GMT file'. I'm following instructions in the lab manual and I cannot figure out what can be wrong.

[bourqueg]

Hi, in module 3 of which workshop exactly?
Thanks.

[veroniquevoisin]

Hi, Do you try to upload GSEA or gProfiler results? Thanks

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On Tue, Apr 11, 2017 at 6:24 AM, petrsha ***@***.***> wrote: Hi, in module 3 lab exercise 2 when building enrichment map I always get error 'No genes in the expression file are found in the GMT file'. I'm following instructions in the lab manual and I cannot figure out what can be wrong. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHODy0zzA81QhAmdpYhtURiZPOohe6L6ks5ru1TtgaJpZM4M55zR> .

-- *Veronique Voisin, PhD* Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. *https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources <https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources>* http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[ghost]

It's 'Pathway and Networks Analysis of -Omics Data 2016'.
I tried gProfiler results.

[bioinformatics-ca]

Hi,

We have an updated version of that tutorial. Can you try following the steps here: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module14_lab_2.

You will need Cytoscape 3.4.0.

Thanks,
Ann

[veroniquevoisin]

Hi, for gprofiler, the .gmt is optional, try without.

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On Tue, Apr 11, 2017 at 2:20 PM, petrsha ***@***.***> wrote: It's 'Pathway and Networks Analysis of -Omics Data 2016'. I tried gProfiler results. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHODy-ko625J6kWqzt4asQWM2UgcZLcnks5ru8RtgaJpZM4M55zR> .

-- *Veronique Voisin, PhD* Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. *https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources <https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources>* http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[ghost]

Thank you. I tried the updated tutorial, but I still have same problem and I don't use .gmt:

 Building Enrichment Map
Parsing GSEA Enrichment Result file
 Parsing Generic Results file - 832 rows
Parsing GCT file
 Parsing GCT file - 14451 rows
 No genes in the expression file are found in the GMT file

[ghost]

And I selected analysis type 'generic/gProfiler' thus I don't understand why is it doing 'Pairsing GSEA Enrichment Result file'..

[veroniquevoisin]

did you upload an expression file? This file is optional as well. Try only the gprofiler result first that you upload in the enrichment result box and let me know (one field below the expression file box) v.

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On Tue, Apr 11, 2017 at 3:27 PM, petrsha ***@***.***> wrote: And I selected analysis type 'generic/gProfiler' thus I don't understand why is it doing 'Pairsing GSEA Enrichment Result file'.. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHODy1koGWZrdWcwlItjNeyGzcpDudC_ks5ru9QMgaJpZM4M55zR> .

-- *Veronique Voisin, PhD* Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. *https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources <https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources>* http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[ghost]

[veroniquevoisin]

please email me your gprofiler file and I will try : veronique.voisin@gmail.com

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On Tue, Apr 11, 2017 at 5:04 PM, petrsha ***@***.***> wrote: [image: image] <https://cloud.githubusercontent.com/assets/27279414/24930766/0317dc64-1f0b-11e7-810b-6078ff7979f3.png> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHODy2UeR0NJsJXAXpSLTPfy80agd7AYks5ru-rBgaJpZM4M55zR> .

-- *Veronique Voisin, PhD* Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. *https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources <https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources>* http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org