rnk files

[Letoto H]

Hello, i try to do a GSEA with my RNA-Seq Data.

I used my excel file with 2 columns (Gene-ID and Fold change) and saved it as .txt-file, then i changed the .txt to .rnk in the characteristics.

When i try to upload this file i get this response "For the ranked list, please upload a 'rnk' file with two columns (ids and scores). " can you help me?

[John Elizarraras]

Hello,

This is most likely because your rank file is in the wrong format. For webgestalt, the rnk file needs have IDs in the first column and the score in the second separated by a tab. In excel, you can do this by saving as a "Tab delimited Text (.txt)" file. Then you have to rename the file ending into .rnk. It sounds like you may have done this already. If you have, you can try double checking that there are no headers or extra columns in the final file. If none of this works, you can select all the rows and columns in Excel and copy-paste it into the gene ID text box in WebGestalt (directly underneath the upload button). It should automatically paste in the tab separated format.

Let me know if this doesn't work or you have any more questions.

Best,

John

[Letoto H]

Thanks for the answer, i tried both way (i checked that there are no headers or extra colums and i copy pasted it into the text both in second try) but got the same result as before.

i uploaded an example of what i tried to upload and what i copy-pastet, did i do something wrong there?

[John Elizarraras]

After some testing, I believe it is throwing an error because of the use of "," as the decimal separator instead of "." . I changed the "," into "." and it worked, and I uploaded the list with these changes. Sorry for the confusion, I will look into making the error clearer.

[Letoto H]

thank you very much, now everything workes just fine. i have one more question, is ist important for GSEA, that my genes are in a ranked order (for example from the highest to the lowest fold change; similar to my attached txt-file) or is it just important, that every gene ID has a related score in my list of genes?

[John Elizarraras]

The order of the genes does not matter, but they should all have a score. Happy to help, and if you have any more questions, let me know!

Best,

John