matrix's fColCnt:6

[zhiheng he]

Hi Anthony,

when I run the GSEA task, I met a incomprehensible error. It always showed this error even if I reduced the number of my samples from 400 to 200.I want to know if this error is related to the number of samples.I am just a graduate student engaged in the biological industry, not a professional programmer, so I can't do anything about this problem.

Wish your help!

Thanks

[Anthony Castanza]

Hello,

 

This error usually occurs when there is a mismatch between how many samples are defined in the CLS file and the number of sample columns in the dataset file.

The CLS format specification is here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29 and likewise the GCT specification is here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

 

If after reviewing the specifications and your input files, you're not able to identify an issue that might have caused this, you can send the data files confidentially to gsea...@broadinstitute.org and I can take a look, and try to reproduce and resolve the error.

 

-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 zhiheng he <hezhi...@gmail.com>
Date: Sunday, August 1, 2021 at 7:32 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] matrix's fColCnt:6

Hi Anthony,

when I run the GSEA task, I met a incomprehensible error. It always showed this error even if I reduced the number of my samples from 400 to 200.I want to know if this error is related to the number of samples.I am just a graduate student engaged in the biological industry, not a professional programmer, so I can't do anything about this problem.

Wish your help!

Thanks

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[zhiheng he]

I have email my data to you mails.Hope you can take a look to help me.

Thanks very much

[Anthony Castanza]

Hello,

I'm not seeing any files at the GSEA-team address, please try resending them. If they still don't come through I'll look into other options.

-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/df48ccad-e806-43e4-9045-1eb78987175en%40googlegroups.com.

[zhiheng he]

Hello,

I have sent my data to gsea...@broadinstitute.org.

Maybe it is not a usual mail for you.