leading edge analysis issues

[Vedran Radojcic]

Just wondering if anyone has advice regarding leading edge analysis html output issues. I cannot get the hyperlinks for gene sets used in analysis ("Details of gene sets and signals used in this analysis") to work and am only getting error message "Your file was not found. It may have been moved or deleted. ERR_FILE_NOT_FOUND".

Thanks

[David Eby]

Hi Vedran,

It's hard to say without more details, but to hazard a guess this might be caused by spaces or other special characters in file names.  

When the report is built, names of items like gene sets are used to name report files, so if those names contain spaces then your web browser might not be able to handle the file path.  That applies to the Analysis Name as well.  We recommend sticking to alphanumeric names with underscores in place of special characters as needed.

The other obvious possibility is that the original GSEA (or Preranked) analysis input to Leading Edge might have been deleted.  The links in the Leading Edge report point back to the original analysis report pages, so the links will be dead if this is deleted.

Hope that helps.!

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

On Tue, Aug 22, 2017 at 8:30 AM, Vedran Radojcic <vedran....@gmail.com> wrote:

Just wondering if anyone has advice regarding leading edge analysis html output issues. I cannot get the hyperlinks for gene sets used in analysis ("Details of gene sets and signals used in this analysis") to work and am only getting error message "Your file was not found. It may have been moved or deleted. ERR_FILE_NOT_FOUND".

Thanks

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[Vedran Radojcic]

I'll try to rerun the analysis to keep the the file relations intact. However, none of the files used to create original report, or report files have been moved or deleted, nor have any special characters been used (pulled from standard msigdbs). Any other suggestions?

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[David Eby]

I can take a closer look at the files if you like.  Can you ZIP and send us both the Leading Edge report directory and the original analysis directory?  These will typically be in the gsea_home/output directory.

You can send them to our private gsea-team address if you don't want them posted in public (see the Contact page on our website).

- David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CANi_cYgN4pG7ep6Wg0wXvH9gWXxKdfssFQe_pWgnwN0ZsOZfXQ%40mail.gmail.com.

[Vedran Radojcic]

Files are too large to send, link to files on google drive are attached.

https://drive.google.com/open?id=0B6K0LWTBHxBkSkRmR0x6am5XVEk

https://drive.google.com/open?id=0B6K0LWTBHxBkMmZxWnlsRXlGMTQ

Vedran

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[David Eby]

Hi Vedran,

GSEA only generates detailed report pages for the Top X up/down-enriched gene sets, as specified by the "Plot graphs for the top sets of each phenotype" Advanced field setting (default 20, but set to 100 in your analysis).

What's happening is that the gene sets in the Leading Edge analysis point are outside that group of Top 100, so there are no corresponding pages.

GSEA should probably skip the link creation in this case.  I'll file a bug-tracking ticket on this so maybe we can fix it in a future release.

- David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CANi_cYjrwbf1BuJRfxfMVQ4kmP%3DD6u1xq4XeektqT%3D1YwPsa6Q%40mail.gmail.com.

[Vedran Radojcic]

Sounds great. I'll look into the position of the GS of interest and expand the criteria when re-running the GSEA.

Thanks

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[Choah Kim]

Hello,

I am having a similar issue opening the gene set hyperlink on the analysis page. None of the hyperlinks seem to work and send me to the ERR_FILE_NOT_FOUND error page. 

I did not move or delete anything and also pulled from msigdb. I would greatly appreciate any help with this.

Thank you.

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[Anthony Castanza]

Could you perhaps provide me with an example of one of the links as your browser is seeing it, as well as the filename of the MSigDB genesets that you used?

One possibility is that you've inadvertently used an old version of MSigDB with an unsupported link format.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Choah Kim]

Here is the link after I click on one of the geneset hyperlinks: file:///Users/ckim/gsea_home/output/jul09/my_analysis.GseaPreranked.1720625055842/edb/HALLMARK_MYC_TARGETS_V1.html
The gene set I used for the GSEA analysis was: ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.2.Hs.symbols.gmt 

Best,

Choah

[Anthony Castanza]

Okay that's quite odd, there shouldn't be a /edb/ in that url, it should simply be

file:///Users/ckim/gsea_home/output/jul09/my_analysis.GseaPreranked.1720625055842/HALLMARK_MYC_TARGETS_V1.html

Did you run GSEA through the UI or from the commandline?

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/b620624b-18ce-4b5f-a57a-b674a47650f4n%40googlegroups.com.

[Choah Kim]

I tried copy pasting the link you sent me without the /edb/ and it seems to work. 

I ran the GSEA through the GSEA application that I downloaded. I noticed that once I open the html file after running the Leading Edge analysis on that GSEA app, at the top, it tells me this: "Leading edge report for GSEA result folder: edb". I'm not sure what this edb folder is since I never intentionally set it to save there--is there a way to change this?

Thank you,

Choah

[Choah Kim]

I actually just found that I am unable to open this hyperlink even though I removed the "/edb/" for it:

file:///Users/ckim/gsea_home/output/jul01/my_analysis.GseaPreranked.1719861605448/KEGG_OXIDATIVE_PHOSPHORYLATION.html

Might there be another way to access this data?

Best,

Choah

[Anthony Castanza]

Hi Choah,

Each time GSEA runs it produces a results folder for the specific run with all the data produced, within that folder is an edb subfolder that contains all the data GSEA needs to reproduce the run as well as a ".edb" file that contains the full set of enrichment data in GSEA's internal database format.

The leading edge analysis tool works by parsing the data from this edb file in the edb subfolder. The issue is that GSEA is producing an incorrect results path in the leading edge analysis run using the edb folder path as the base instead of the correct file path that should start one directory up.

When you ran leading edge analysis did you use the option to select a GSEA run from the application cache or did you manually select the results folder you wanted to analyze? Figuring out exactly how this happened will help us get the bug fixed.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/18f32ec5-fea8-48d5-9886-48db88eb5dcbn%40googlegroups.com.

[Choah Kim]

Hi Anthony,

I selected a GSEA run from the application cache in order to run leading edge analysis.