GSEA Gene Cluster Text File Format error

[Ming-yi Chung]

Hi Anthony,

Sorry for using the CONTACT on GSEA-MSigDB Documentation for Q&A.

I changed the file extension to .gct, and then it worked. If it remained as .txt, the error still existed, as shown below for your information.

Your assistance is greatly appreciated.

Kind regards,

Ming-yi

On Sat, Jun 8, 2024 at 3:29 AM Anthony Castanza wrote:

Hi Ming-yi, that change will not result in a proper parsable GCT file, if that change worked then there is something else wrong with your file formatting that is causing it to erroneously be parsed without error.

The proper formatting for the GCT format is described here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

I'd also note that this mailing address is intended for gene set submissions, not for other support with GSEA. the GSEA-Help google group is the proper location for support inquiries.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

On Thu, Jun 6, 2024 at 2:30 AM wrote:

Hi,

I am using GSEA for the first time. Following file format guidelines (Data Formats - GSEA-MSigDB Documentation), I encountered a "java.lang.NumberFormatException: For input string: "Description"" error. This error was solved by combining rows 1 and 2, that is, 

originally, 

#1.2

1000       130

should have been

#1.2      1000       130

Thank you all for developing GSEA, a powerful and wonderful tool for analyzing expression data.

Kind regards,

Ming-yi