gsea-help

Just an update: for longer-term stability, these arrays have been moved to our Legacy Annotations

Hello Mai, I would encourage you to first examine the user guide we offer, particularly the section

Hi Thomas, Our apologies for the spam email that slipped through our filters over the weekend. To

Hi Anthony, Thanks for that information. I think you were right. I tried using a continuous phenotype

Hi Arko, The plot with red and blue squares is a row normalized heatmap of the expression from your

Hi Anthony, Thanks a lot for your feedback. Yes, there is an interesting trend for that gene set in

Great, thanks for the info. Just wanted to make sure I wasn't do anything wrong. On Tuesday, May

The Human collections are generally more comprehensive than the Mouse collections, however if you are

You would need to make sure you're running gene_set permutation mode, those parameters are cut

Hi Aldo, Thanks for pointing this out. It turns out that there was an extra stray double-quote around

Hi Nancy, The issue here is that GSEA is failing to parse the mounted file path from the google drive

Hi Kevin, Sorry for the delay getting back to you. The GSEA's FDR is not just a corrected pValue.

Hi Theo, We provide json formatted versions of MSigDB gene sets on our downloads page that have all

Hi Miguel, Here's a link to our license for GSEA Desktop. It's a BSD-style license, and

Hello, It looks like GSEA encountered an unexpected character value (a ? Symbol) where it expected a

Hi David, First of all, thank you so much for your response—it was extremely helpful! I've been

Hi Marcia, This would appear to be a structural issue with one of your dataset files. Could you

Hi, I just started learning how to use GSEA. I finally have the files uploaded but when I click run I

They updated it seems. But also, there is this line that gives a plot twist: One can also omit this

Hi Parwez, Unfortunately without more information the amount of help I can provide is limited. Please

Hello, Yes you are correct, this would appear to be an upstream annotation error in the parent GTRD

Thank you. Got it. It works. Kind Regards GOLAM Iftakhar Khandakar On Wednesday, April 9, 2025,

Great! I just sent the files to the email address. Thank you so much! Jinoh On Tuesday, April 1, 2025

It helped a lot, Anthony. Thank you, Lilian Em quinta-feira, 3 de abril de 2025, Anthony Castanza

Hi Jinoh, Yes, you can send your file to gsea...@broadinstitute.org and we can confidentially

Hi Antony, thank you very much for your answer. I referred to the same hallmark-associated

Hi, Unfortunately there are issues with the service that GSEA uses to retrieve the files from their

Hi Olga, Unfortunately there are issues with the service that GSEA uses to retrieve the files from

Hi Hao, Unfortunately there are issues with the service that GSEA uses to retrieve the files from

Hi Hamed, The error here is because your gct file was saved as UTF-16 encoded text which is not

Found it, thank you! On Monday, March 17, 2025 at 5:05:36 PM UTC-7 Anthony Castanza wrote: Hi Nick