How to create an .rnk file

[Nicola Chiarelli]

Hi,

I cannot create a file with the required .rnk format. Can you give me a model / example.
Thanks in advance
Nicola

[Anthony Castanza]

Hello,

 

The .rnk file format is a simple two column tab delimited text format where the first column is the gene identifier and the second column is the ranking value for each gene. The general expectation is that the file contains the ranking information for all expressed genes.

The filename must end with “.rnk” not “.rnk.txt” the .txt file extension is frequently hidden by operating systems and can cause issues here.

 

The format specification is defined here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29

 

In what way are you unable to create a file with the required format? Is GSEA giving a particular error?

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Nicola Chiarelli]

Hi Anthony,

thanks for the quick response.

GSEA using WebGestalt toolkit gives the following error: The format of the uploaded ranked list is incorrect. Please make sure the file contains two column of gene IDs and scores. I created (by excel)  a first column with the gene_symbol (heading omitted) and the second column with the fold-change. I saved excel in txt, and next changed the extension file from .txt to .rnk. Is this the correct procedure?

Nicola

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[David Eby]

Hi Nicola,

Did you still need help with this?  That procedure sounds correct, so if you are still having errors you might want to forward the file to us to take a closer look.  You can send it to gsea...@broadinstitute.org which will keep it private.

Note that there are certain possible pitfalls in using Excel to handle genomics dataset files, in particular that it will often try to "auto-correct" gene names into dates or other values (like SEPT1 to Sep-01 for example).  It might also tack on extra rows or columns that are empty, just due to whatever you were doing in the spreadsheet before saving.

Regards,

David

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

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[Nicola Chiarelli]

Thanks. I'm solved the error.

Best wishes

Nicola

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[wala alzboun]

Hi,

I have the same problem right now. I was wondering, how did you solve it out?

Many thanks

Walla

[Aleksandra K]

Hello,

I got the same problem here - I try to save my list from excel as*.rnk but it is saved as default as *.rnk.txt and I am not able to change it. I will be really grateful for any hint :)

best regards,

Ola

[Anthony Castanza]

Hi Ola,

This is unfortunately an Excel issue. You should be able to open the file properties and remove the .txt extension manually.

That said, try loading the file into GSEA anyway. We don't advertise support for this but in more recent versions of GSEA we've made some improvements to the file parser that should allow these double file extensions to be parsed correctly (assuming no other errors in the file formatting).

-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/77d529fb-936e-43ed-969a-564ca156c507n%40googlegroups.com.

[Aleksandra K]

Hi Anthony

,

thanks for the tips, since then I ve been using Libre office fot this and it works:)

I have general question about GSEA on Affymetrix HTA 2.0 microarray data (not sure if to post it here) - I encounter some issues with GSEA, genepattern and EM visualisation and would really appreciate help with these:)

Best regards,

Ola