Error in GCT file to perform GSEA

Question

[Amr]

I created GCT file manually on Excel of normalized count matrix to perform GSEA:

While I am uploading the gct file on GSEA software: I always get that error :

java.lang.NumberFormatExceptions: for input string "24388,4,,,,"

The GCT file description is: In the top left cell in the first row i entered #1.2 in the second row for the first cell I entered the number of genes inside which is 24388 (rows), the second cell in second row i entered the number of samples 4 in the third row in the first column I entered Name as column name for the gene ensemble IDs, in the third row in the second column i entered desc and all values are N/A Then in the third, fourth fifth and sixth columns I entered the samples with the name and their values.

Is there any solution? why I get that error? any alternative solutions than performing gct manually are also welcome....Thanks

[Pierre Lindenbaum]

"24388,4,,,,"

looks like a CSV file, are you sure GSEA uses CSV files and/or not TSV files ?

[Amr]

I renamed the file with the extension .gct , to convert it to gct file

[rpolicastro]

Changing the extension of the file doesn't change the file format.

[Amr]

So what should be done? Do you have an idea?

[Pierre Lindenbaum]

answer the question:

are you sure GSEA uses CSV files and/or not TSV files ?

[Amr]

I opened the file in CSV, I did the changes, then I saved the file as .gct extension, do you think the problem is here ? If yes then How to change the file extension? Thanks

Answer 1

[Amr]

The problem was in the desc column, it should be Description !!! problem solved !!