GSEA Must be finite.

Question

[yueli7]

Hello,

I tried to use GSEA to generate mountain graph.

ERROR: Trouble saving image java.lang.IllegalArgumentException: Must be finite.

I think the input number is infinite.

So how I can figure out this problem?

Thanks in advance for any help!

Best,

Yue

Answer 1

[Mark]

This could be a bug in the software: https://github.com/GSEA-MSigDB/gsea-desktop/issues/14

I suggest trying different gene enrichment analysis software or an older version of GSEA (not version 4.0)

[yueli7]

Thank you so much!

I will try to install the old version of GSEA, (not version 4.0)

Thank you again!

Yue

[yueli7]

Hello, Amar,

Thank you so much for your help!

May I ask where I can download the old version of GSEA?

https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/3.0/

There is nothing in this folder.

Thank you in advance for your great help!

Best,

Yue

[Mark]

There's a .jar file in the link you provided. https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/3.0/gsea-3.0.jar

[yueli7]

Hello, Amar,

Thank you so much for your help!

cd gsea

java -jar gsea-3.0.jar

Thank you again！

Best,

Yue

[yueli7]

Just add 0.8 in each number (column or row). 0.8 is a pseudocount, just not let any number to be 0.