GSEA 4.3

[Ayça Nazli]

Hello,

I've been using 4.1 and 4.2 versions on MacBook Pro and Windows 10 and had absolutely no problem with anything. Yesterday I downloaded 4.3 and now for some reason it says "Selected CHIP is not compatible with the selected gene set(s) species". I use exactly same data, I was trying to double check my results before submitting them for a paper. This is the problem I have on Windows 10, on MacBook Pro it doesn't even load the files I have. And when I tried this on another Windows 10 computer it run and finished with some warnings. I am using exactly same files and settings, I don't understand why is this happening. Can anyone help me with this?

[Anthony Castanza]

Hello,

The latest version of GSEA introduced new gene set database files and chip files to support native analysis of mouse data, this error should only occur when attempting to mix-and-match between the gene sets from the human database and chip files from the mouse database or vice versa.

These files are now split into two different tabs in both the GSEA gene sets and chip files UI windows. The first tab in both windows contains the classical human database files. For the gene sets window this is gene set files in human gene symbols, the second tab contains the mouse native gene sets we recently introduced. For the chip window it follows the same format. The first tab contains all the chips that target the human database, chips for human data as well as orthology chips for mouse and rat, the second tab contains chips that target the mouse database including orthology chips for human and rat.

What database the files belong with can be determined by their suffix. 2022.1.Hs files are part of the human database and 2022.1.Mm files are part of the mouse database. If you select a gene set from 2022.1.Hs you must select a chip from the Human chips tab that ends in 2022.1.Hs as well - as I mentioned this tab also still includes chip files for converting mouse and rat data to human orthologs to run against the 2022.1.Hs (human) gene set.

This error should never occur on manually loaded data.

Could you please double check the gene set database file and chip file names that you've selected?

If everything still appears correct, please copy the full file path from the UI and send it to us here as well as any other information or screenshots of the UI that might be needed to try to reproduce this error.

-Anthony

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

On Thu, Sep 15, 2022, 8:15 AM Ayça Nazli <ayca.r...@gmail.com> wrote:

Hello,

I've been using 4.1 and 4.2 versions on MacBook Pro and Windows 10 and had absolutely no problem with anything. Yesterday I downloaded 4.3 and now for some reason it says "Selected CHIP is not compatible with the selected gene set(s) species". I use exactly same data, I was trying to double check my results before submitting them for a paper. This is the problem I have on Windows 10, on MacBook Pro it doesn't even load the files I have. And when I tried this on another Windows 10 computer it run and finished with some warnings. I am using exactly same files and settings, I don't understand why is this happening. Can anyone help me with this?

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[David Eby]

Hi Ayça,

We were able to reproduce what we think is the same bug through an independent report.  Are you running with one of the MSigDB Chip files at the same time as using the Load Data screen to load a GMT from your own computer (local file access)?  There is indeed a bug here, and I have a fix in the works, which should be ready in the next couple of days.

As a workaround until then, you can download the MSigDB Chip file directly from our website and then also use Load Data to load it into GSEA.  After that it will be accessible from the Local Chips tab of the Chip selector.  Those files are available on the Downloads page through the links at the bottom of the page.  Note that the Human Chips have a separate link from the Mouse Chips and should be used in the way Anthony outlined earlier.

Thanks,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CAGCeyZy5rPFcBianYTiv8Y4Snry-acNtyYrDMkZdHE7ANSBOBw%40mail.gmail.com.

[Ayça Nazli]

Thank you so much for all the help. I was careful with human vs mouse data to not mix those because we also have both data sets and it's important to provide separate results. I was doing exactly what you described as loading my own gmt file and using MSigDB chip files. When i downloaded it from the web site and manually loaded to GSEA it worked. Thank you so much for all the help and I'll be waiting for the fix.
Thanks,

15 Eylül 2022 Perşembe tarihinde saat 19:05:41 UTC-5 itibarıyla David Eby şunları yazdı:

[Ayça Nazli]

Can you also help me with loading problem I have on macbook pro? When i try to load my files (they work on a Windows 10 computer), i receive this message;
<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:5
Parsing trouble
java.lang.IllegalArgumentExcepti ...

---- Stack Trace ----
# of exceptions: 5
------Unknown file format: Combmouse.txt no known Parser for ext: ------
java.lang.IllegalArgumentException: Unknown file format: Combmouse.txt no known Parser for ext:
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)


------Unknown file format: Breast_cancer.gmt no known Parser for ext: ------
java.lang.IllegalArgumentException: Unknown file format: Breast_cancer.gmt no known Parser for ext:
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)


------Unknown file format: Comb.cls no known Parser for ext: ------
java.lang.IllegalArgumentException: Unknown file format: Comb.cls no known Parser for ext:
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)


------Unknown file format: Combs2.txt no known Parser for ext: ------
java.lang.IllegalArgumentException: Unknown file format: Combs2.txt no known Parser for ext:
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)


------Unknown file format: Human_Ensembl_Gene_ID_MSigDB.v2022.1.Hs.chip no known Parser for ext: ------
java.lang.IllegalArgumentException: Unknown file format: Human_Ensembl_Gene_ID_MSigDB.v2022.1.Hs.chip no known Parser for ext:
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)

17 Eylül 2022 Cumartesi tarihinde saat 11:23:56 UTC-5 itibarıyla Ayça Nazli şunları yazdı:

[David Eby]

Hi Ayça,

That message suggests that there is some kind of additional unrecognized extension on the Combs2.txt file name.  GSEA uses the file name extension (.txt, .cls, .gct, etc) to decide how to parse the file and this one has an extension it does recognize.  In fact, the error message seems to suggest the file name might be "Combs2.txt." with an extra '.' on the end, though I can't be sure.

Some operating systems are set to hide file extensions by default and so you might not be able to see this.  You can use these instructions from Apple to show the file extensions and make sure there is nothing present beyond the ".txt".

- David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/1601c08f-7b8d-433c-8cfc-3c842c2b6d73n%40googlegroups.com.

[Ayça Nazli]

Thank you very much for the response. I checked all of them and made sure they are as they appear and there is nothing after the extension and they are .txt .gmt .cls but I still cannot load the files.

17 Eylül 2022 Cumartesi tarihinde saat 13:36:17 UTC-5 itibarıyla David Eby şunları yazdı:

[David Eby]

Hi Ayça,

Apple has been tightening security in recent macOS releases and has added restrictions on loading files from certain locations, in particular the Desktop, Documents, Downloads folders.  Are these files in any of those locations?

We have made adjustments to GSEA to allow loading from there, but it's possible that we missed some details.  There are multiple ways to load files in GSEA.  How exactly are you trying to load them?

It also might be helpful for us to see the actual files; you can send them to our private support address at gsea...@broadinstitute.org.

Thanks!

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/6c304a30-2e84-404d-b07e-cfafac717089n%40googlegroups.com.

[David Eby]

Hi Ayça,

I also wanted to let you know that we've released GSEA Desktop 4.3.1 which fixes the issue you first noticed in matching the species of the CHIP with the gene sets.

Thanks!

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

[Giovanna Mantica]

Hello, 

I fear I am having a similar problem, but I was not able to understand from the above thread how to fix it. I am running GSEA on a ranked list of mouse genes, using a human gene-set database. I use as Chip platform the Mouse_Gene_Symbol_Remapping_Human_Orthologs_MSigDB.v2023.Hs.chip
and, regardless if the gene set database is locally loaded or not, I get the error "the selected CHIP does not match the version of the MSigDB collection selected. Some gene identifiers may not be mapped". The analysis then proceeds, but I am not sure if I have some gene symbol that is not mapped. Can you direct me in how to solve the issue? Thanks a lot!

[David Eby]

Hi,

Thanks for the report.  We'll be looking to update these error messages and the conditions that trigger them in the future.

The key thing to know is that, provided you have obtained both the CHIP and the GMT file from our servers and their versions match (e.g. the '2023.1.Hs' or '2023.1.Mm' part), then you can ignore this warning.  This warning is just meant to check whether you are using a mix of Human and Mouse files, or files from different MSigDB versions.  It's quite possible that there's a bug in the check, however.

While it is still possible that you may have gene symbols in your dataset that are unmapped, it won't be due to the conditions this warning is checking.  For example, if you've chosen the wrong CHIP for your namespace then there will be unmapped symbol.

I hope this helps,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/62b59526-b5e0-4825-8247-529108109a2en%40googlegroups.com.

[Hao]

Hello,

Recently I have seen this error message when I wanted to select a gene set from Gene sets database.

• Error listing MSigDB files:
• Connection timed out: connect
• 
  
• This might be due to your network's firewall rules.
• MSigDB files can be manually downloaded from www.gsea-msigdb.org/gsea/downloads.jsp
• 
  
• Use 'Load Data' to provide access to local files.
• Choose gene sets from other tabs.

It also happened to my colleagues. Apparently, we had no problem a few days before. 

I am wondering if anyone had this error message, and how this can be fixed. 

Thank you for the help.

Hao 

[Helga Thorvaldsdottir]

Hi Hao,

Unfortunately there are issues with the service that GSEA uses to retrieve the files from their hosted location. We have contacted the IT group that maintains the service and they are looking into it.

In the meantime, please follow the instructions in the error message to download the gene set and chip platform files you are interested in and have GSEA use the local copies.

Helga