.chip file issues

[Monica Koubeck]

Hi everyone, 

I am trying to run GSEA and all my files are working except for my chip file. I have two issues: 

1. Issues saving it as a .chip file. I originally used excel to create the format and exported it as "Chip1.chip", but saved it as a .txt file since my computer couldnt save it just as a .chip file, and now I cannot get my computer to remove the .txt file extension ( I have read on other forums but none of their suggestions (renaming, resaving) helped unfortunatley).

2. Issues loading the chip file into GSEA (could be related to the above issue). When I try to upload it to GSEA I get this error: 

-For input string: ""steroid biosynthetic process|ergosterol biosynthetic process|steroid metabolic processs""

at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

Even though from my understanding the last column of a chip file should have text (not numbers). An example of the format of my chip file is below:

Any help would be super appreciated, I am super new to GSEA and analyzing gene sets in general, and although I looked through this forum and others I am having trouble finding solutions that work!

Thank you!!

Monica 

[Anthony Castanza]

Hi Monica,

 

You’re getting an error message because GSEA can’t parse the chip file if it has a txt extension. GSEA uses the .txt extension for a particular kind of expression data file.

On windows there’s a setting under view called “show file extensiosn for known file types” or something of that nature that should let you see the .txt extension.

On Macs there’s a similar option under Finder’s Preferences > Advanced > Show all filename extensions”

You should also be able to see the .txt extension in the file’s properties or get info window depending on your OS. Once you delete the .txt extension and your file ends with .chip only, it should load into GSEA (or at least give a different, chip specific error message which, if it happens, we can debug then).

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

 

 

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Monica Koubeck <meko...@gmail.com>
Date: Tuesday, June 1, 2021 at 5:31 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] .chip file issues

Hi everyone, 

 

I am trying to run GSEA and all my files are working except for my chip file. I have two issues: 

1. Issues saving it as a .chip file. I originally used excel to create the format and exported it as "Chip1.chip", but saved it as a .txt file since my computer couldnt save it just as a .chip file, and now I cannot get my computer to remove the .txt file extension ( I have read on other forums but none of their suggestions (renaming, resaving) helped unfortunatley).

2. Issues loading the chip file into GSEA (could be related to the above issue). When I try to upload it to GSEA I get this error: 

-For input string: ""steroid biosynthetic process|ergosterol biosynthetic process|steroid metabolic processs""

at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

 

Even though from my understanding the last column of a chip file should have text (not numbers). An example of the format of my chip file is below:

 

Any help would be super appreciated, I am super new to GSEA and analyzing gene sets in general, and although I looked through this forum and others I am having trouble finding solutions that work!

Thank you!!

 

Monica 

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[Monica Koubeck]

Hi Anthony, Thank you so much for your help! Going to the view tab on and using the "show file extension" let me delete the .txt so all my files now load into GSEA (and its a good trick to know!) Appreciate your quick response!

Monica 

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