How to view the enrichment plots

[Fenghua Qian]

Hi there,

I’m sending this email to ask if it’s possible to show more than 20 enrichment plots in GSEA report. When I click “snapshot” in the report, I can only view at most twenty enrichment plots. However, I’d like to use some plots in the gene sets not shown. Please let me know what I can do to fix it.

Thank you.

[Anthony Castanza]

Hello,

 

On the Run GSEA page, under “Advanced fields” there is a parameter “Plot graphs for the top sets of each phenotype”. By default this is set to 20 but it can be set to any arbitrary integer. Additionally, in order to ensure that your results are identical to the previous run, you’ll want to open the index.html page creted by your previous run and scroll down to the bottom where under “Comments” there is the text “Timestamp used as random seed” and a numerical value. That numerical value should be copied to the “Seed for permutation” advanced field (replacing the default “timestamp” text).

 

Let me know if this doesn’t work for you,

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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[Chen and Vanessa]

I changed the default set to 50 and pasted my number of "Timestamp used as random seed" in the "Seed for permutation". And then clicked "Run". But it shows "Error!" 

[Fenghua Qian]

I changed the default set to 50 and pasted my number of "Timestamp used as random seed" in the "Seed for permutation". And then clicked "Run". But it shows "Error!" 

[Anthony Castanza]

Hello,

What is the precise error message you received? You might need to look in the GSEA application messages dialogue to find this (the + button next to the time at the bottom left).

Also, be careful that the number was pasted without any spaces.

-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/1f705e3e-a90a-4ab3-8345-244b883d4e0fn%40googlegroups.com.

[Fenghua Qian]

Here is the description

[Anthony Castanza]

Based on this error it looks like you didn't reload the rest of the parameters from the previous job that you're trying to reproduce. You'll need to set up the new job just as the old job was previously except for the two advanced parameters. Sorry if this wasn't clear in my initial response.

-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/5f5fec0b-236a-490e-b43a-61782a41588fn%40googlegroups.com.

[Fenghua Qian]

I see. I can do that. Thank you so much.