gsea-help

Hi Hye, You generally do not want to use the GSEA_R code, it is extremely old and no longer

Hi Hamed, If you're running the Leading Edge Analysis from the Leading Edge tool in the GSEA

Hi Hamed We don't really make a specific recommendation on NES based cutoffs, we suggest using

Hi Nupur, The NES value is calculated from the true enrichment score and the null distribution

Hello, Its extremely difficult to determine what the error might be from a copy and paste of the file

Hi Manjunath You should include all genes, not just those that pass an arbitrary p-value cutoff. GSEA

Hello, It looks like the GMT file produced by g:profiler is improperly formatted using comma

Looks like those warnings can be safely ignored in your case. -Anthony Anthony S. Castanza, PhD

No. The enrichment score is always reported with respect to the positive phenotype, in this case 16e6

Hello, These appear to be Human Gene Symbols, so the Human Gene Symbol with Remapping CHIP file

Hello, The default “signal_to_noise” ranking metric requires a minimum of three samples per group,

Hi Mehwish, For GSEA generally we recommend an expression file containing the full normalized read

Dear Anthony, I used edgeR to normalize my data. So, I have raw_count, read_count, CPM (TMM). So, as

Hi Tom, If this happens every time you try to use GSEA, the likely cause is that your IT organization

Thankyou Anthony .. Really appreciate your help.. On Friday, 12 May 2023 at 12:56:17 UTC-5 Castanza,

Hi Martin, My apologies for missing your question it somehow slipped through the cracks.

Dear GSEA Help Community, My name is Ferenc Kagan, and I am a metabolomics researcher at Medipredict.

Hi Oğuzhan, That is odd, I would wonder if there is some batch effect or other confounding variable

Hi Anthony, Thanks for the response, I'll keep this in mind. Cheers! Regards, Adel On Tuesday,

Hi Vithurran, You can send your files to gsea...@broadinstitute.org, that is the best way to send

Hi Thorben No, I haven't heard anything back from the author. If we're unable to get a

Hi Allyson, You would want to include the full list of all expressed genes, not just those that were

Thank you so much! On Thursday, May 4, 2023 at 2:38:45 AM UTC+10 Castanza, Anthony wrote: Hello, GSEA

Hello, Yes you're correct. In order to use the MSigDB Ensembl Gene ID chip files you need to trim

Hi Sana, GSEA Preranked would be the way to run this data, however, it only supports ranking by a

In order to calculate significance statistics for enrichment results, GSEA needs to generate a null

Hi Fercho, There are a couple issues here, first, GSEA expects data for all genes that would be

Hello, I hope you can help me. I am having the following problem and I have loaded my gct and cls

Hi Leo, The code that you have sent is for fgsea, which is an independent implementation and not

Hi Clara, Can you be more specific about the issues you are seeing? Are you getting an error message?