Can't upload the input file in GSEA-Preranked

shamima

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Apr 22, 2022, 3:21:34 PM4/22/22

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Hi all,

I am using GSEA-Preranked for my bulk RNA seq data. But I am not able to upload my ranked file under the “Ranked list” icon (attached). I saved my ranked file as a .csv format (attached).
Kindly help me out to identify the possible cause that I am not able to upload my gene list. Also, please confirm me that my created file format is okay to use.

Thanks so much for your help in advance.

Best,

Shamima

Anthony Castanza

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Apr 22, 2022, 3:45:34 PM4/22/22

to gsea...@googlegroups.com

Hello,

GSEA does not support CSV, the data file should be saved as "Tab delimited text (.txt)"
Additionally, the "gene_symbol" cell should be changed to "# gene_symbol" (no quotes) so that it gets properly recognized as a header line.

Also, the Remap_only collapse mode is not recommended and will probably not work for Mouse datasets, we recommend the "Collapse" option due to multimappings that occur between the mouse and human genomes.

Let me know if you still have issues after saving as tab delimited text instead of csv.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of shamima <shammi...@gmail.com>
Date: Friday, April 22, 2022 at 12:21 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Can't upload the input file in GSEA-Preranked

Hi all,

I am using GSEA-Preranked for my bulk RNA seq data. But I am not able to upload my ranked file under the “Ranked list” icon (attached). I saved my ranked file as a .csv format (attached).
Kindly help me out to identify the possible cause that I am not able to upload my gene list. Also, please confirm me that my created file format is okay to use.

Thanks so much for your help in advance.

Best,

Shamima

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shamima

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Apr 22, 2022, 4:47:19 PM4/22/22

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Hi Anthony,

Thank you so much for your reply.

Still "Ranked list" icon doesn't work to upload any file. Basically it doesn't show any thing when i click in here.

I change my input file format as you recommended.

Thanks

Anthony Castanza

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Apr 22, 2022, 4:57:55 PM4/22/22

to gsea-help

Hello,

Did you make sure to remove the .txt file extension and replace it with .rnk? A file with the mixed .rnk.txt extension won't work and this sometimes occurs if your operating system is configured to hide known file extensions by default.

Once the file has just the .rnk extension you should be able to load it through the GSEA load data panel and then it should appear in the drop-down.

-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/141cbe03-5520-4ec6-bc5b-9dcb217aedbbn%40googlegroups.com.

shamima

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Apr 22, 2022, 5:23:31 PM4/22/22

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Thank you Anthony

Now it's working but i got an error and it says "The collapsed dataset was empty". Please see the attached.

Best regards,

Shamima

Anthony Castanza

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Apr 22, 2022, 5:33:54 PM4/22/22

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Oh, I missed this in your previous screenshots, you've selected the Mouse_Ensembl_Gene_ID chip but these are not Ensembl Gene IDs, these are Mouse Gene Symbols so you'll need to select the Mouse_Gene_Symbol_with_Remapping chip. Mouse Ensembl Gene IDs have the format ENSMUSG000012345

-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/707d0344-d805-44c3-8ea3-ee826eb46cecn%40googlegroups.com.

shamima

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Apr 22, 2022, 5:47:43 PM4/22/22

to gsea-help

I got the results.

Thank you so much for your help.

Best,

Shamima

shamima

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Apr 22, 2022, 6:24:07 PM4/22/22

to gsea-help

Hi Anthony,

I have attached the demo figure that i wanted to create for my current data. Kindly help me to figure out this kind of plot from GSEA results.

Thanks again for help

-Shamima

Anthony Castanza

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Apr 22, 2022, 7:18:43 PM4/22/22

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Hello,

This is not a plot that was produced by the GSEA software, it was likely produced manually from the result and input files

Sorry I couldn't be more help here

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of shamima <shammi...@gmail.com>
Date: Friday, April 22, 2022 at 3:24 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: Re: [gsea-help] Can't upload the input file in GSEA-Preranked

Hi Anthony,

I have attached the demo figure that i wanted to create for my current data. Kindly help me to figure out this kind of plot from GSEA results.

Thanks again for help

-Shamima

On Friday, April 22, 2022 at 4:47:43 PM UTC-5 shamima wrote:

I got the results.

Thank you so much for your help.

Best,

Shamima

On Friday, April 22, 2022 at 4:33:54 PM UTC-5 Anthony Castanza wrote:

Oh, I missed this in your previous screenshots, you've selected the Mouse_Ensembl_Gene_ID chip but these are not Ensembl Gene IDs, these are Mouse Gene Symbols so you'll need to select the Mouse_Gene_Symbol_with_Remapping chip. Mouse Ensembl Gene IDs have the format ENSMUSG000012345

-Anthony

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

On Fri, Apr 22, 2022, 2:23 PM shamima <shammi...@gmail.com> wrote:

Thank you Anthony

Now it's working but i got an error and it says "The collapsed dataset was empty". Please see the attached.

Best regards,

Shamima

On Friday, April 22, 2022 at 3:57:55 PM UTC-5 Anthony Castanza wrote:

Hello,

Did you make sure to remove the .txt file extension and replace it with .rnk? A file with the mixed .rnk.txt extension won't work and this sometimes occurs if your operating system is configured to hide known file extensions by default.

Once the file has just the .rnk extension you should be able to load it through the GSEA load data panel and then it should appear in the drop-down.

-Anthony

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

On Fri, Apr 22, 2022, 1:47 PM shamima <shammi...@gmail.com> wrote:

Hi Anthony,

Thank you so much for your reply.

Still "Ranked list" icon doesn't work to upload any file. Basically it doesn't show any thing when i click in here.

I change my input file format as you recommended.

Thanks

On Friday, April 22, 2022 at 2:45:34 PM UTC-5 Anthony Castanza wrote:

Hello,

GSEA does not support CSV, the data file should be saved as "Tab delimited text (.txt)"
Additionally, the "gene_symbol" cell should be changed to "# gene_symbol" (no quotes) so that it gets properly recognized as a header line.

Also, the Remap_only collapse mode is not recommended and will probably not work for Mouse datasets, we recommend the "Collapse" option due to multimappings that occur between the mouse and human genomes.

Let me know if you still have issues after saving as tab delimited text instead of csv.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of shamima <shammi...@gmail.com>
Date: Friday, April 22, 2022 at 12:21 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Can't upload the input file in GSEA-Preranked

Hi all,

I am using GSEA-Preranked for my bulk RNA seq data. But I am not able to upload my ranked file under the “Ranked list” icon (attached). I saved my ranked file as a .csv format (attached).
Kindly help me out to identify the possible cause that I am not able to upload my gene list. Also, please confirm me that my created file format is okay to use.

Thanks so much for your help in advance.

Best,

Shamima

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Anthony Castanza

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Apr 25, 2022, 6:21:30 PM4/25/22

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Hello,

If the file isn't showing up in the dropdown, it likely has an incorrect file extension. The file extension should be just .rnk if it has an extra .txt after it, even one hidden by the operating system, it will not appear in the dropdown.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of shamima <shammi...@gmail.com>
Date: Friday, April 22, 2022 at 1:47 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: Re: [gsea-help] Can't upload the input file in GSEA-Preranked

Hi Anthony,

Thank you so much for your reply.

Still "Ranked list" icon doesn't work to upload any file. Basically it doesn't show any thing when i click in here.

I change my input file format as you recommended.

Thanks

On Friday, April 22, 2022 at 2:45:34 PM UTC-5 Anthony Castanza wrote:

Hello,

GSEA does not support CSV, the data file should be saved as "Tab delimited text (.txt)"
Additionally, the "gene_symbol" cell should be changed to "# gene_symbol" (no quotes) so that it gets properly recognized as a header line.

Also, the Remap_only collapse mode is not recommended and will probably not work for Mouse datasets, we recommend the "Collapse" option due to multimappings that occur between the mouse and human genomes.

Let me know if you still have issues after saving as tab delimited text instead of csv.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of shamima <shammi...@gmail.com>
Date: Friday, April 22, 2022 at 12:21 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Can't upload the input file in GSEA-Preranked

Hi all,

I am using GSEA-Preranked for my bulk RNA seq data. But I am not able to upload my ranked file under the “Ranked list” icon (attached). I saved my ranked file as a .csv format (attached).
Kindly help me out to identify the possible cause that I am not able to upload my gene list. Also, please confirm me that my created file format is okay to use.

Thanks so much for your help in advance.

Best,

Shamima

--

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To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/49acec16-eb33-4d70-83d3-da0b9d41c2ben%40googlegroups.com.

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