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bioinformatics-ca / bioinformatics-ca.github.io

Student website repo for 2015/2016 Canadian Bioinformatics Workshops
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Error when building enrichment map #2

Open ghost opened 7 years ago

ghost commented 7 years ago

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 commented 7 years ago

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

veroniquevoisin commented 7 years ago

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

On Tue, Apr 11, 2017 at 6:24 AM, petrsha notifications@github.com 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 https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/issues/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 commented 7 years ago

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

bioinformatics-ca commented 7 years ago

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 commented 7 years ago

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

On Tue, Apr 11, 2017 at 2:20 PM, petrsha notifications@github.com 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 https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/issues/2#issuecomment-293354891, 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 commented 7 years ago

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 commented 7 years ago

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

veroniquevoisin commented 7 years ago

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.

On Tue, Apr 11, 2017 at 3:27 PM, petrsha notifications@github.com 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 https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/issues/2#issuecomment-293374426, 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 commented 7 years ago

image

veroniquevoisin commented 7 years ago

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

On Tue, Apr 11, 2017 at 5:04 PM, petrsha notifications@github.com 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 https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/issues/2#issuecomment-293399283, 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