Error: col:3 > matrix's fColCnt:3

[Pooja Gulhane]

Hello,

I am trying to analyze the gene expression data using GSEA. I have prepared the .gct, .gmt and .cls files accordingly; which have been loaded successfully without error. 

But while running the GSEA a continuous column error is popping up, I have tried all the ways to solve it. 

Could you please help me with a solution to solve the problem.. 

Please find the screenshots of the files and error below.

Error image:

GCT File

Class File

[Anthony Castanza]

Hello,

 

There are a couple problems here, first, the GCT specification doesn't include an EntrezID column, that column should be omitted. Secondly your GCT only contains two samples which doesn't match the sample information described in the CLS. The CLS format expects that there be one entry on the third line for each sample.

Additionally, based on the values in the GCT file, it would appear that this is some kind of pre-computed metric for two groups of samples, GSEA really expects the underlying expression data for each sample in each group.

 

I would suggest reviewing the GCT and CLS format specifications here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

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

 

as well double checking what kind of input data you're using.

 

If you have additional questions, please let us know!

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

 

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Pooja Gulhane <poojagu...@gmail.com>
Date: Monday, March 21, 2022 at 3:40 AM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Error: col:3 > matrix's fColCnt:3

Hello,

 

I am trying to analyze the gene expression data using GSEA. I have prepared the .gct, .gmt and .cls files accordingly; which have been loaded successfully without error. 

 

But while running the GSEA a continuous column error is popping up, I have tried all the ways to solve it. 

Could you please help me with a solution to solve the problem.. 

 

Please find the screenshots of the files and error below.

 

Error image:

 

GCT File

 

 

 

Class File

 

 

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